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In breeding programs, the demand for high-throughput phenotyping is substantial as it serves as a crucial tool for enhancing technological sophistication and efficiency. This advanced approach to phenotyping enables the rapid and precise measurement of complex traits. Therefore, the objective of this study was to estimate the correlation between vegetation indices (VIs) and grain yield and to identify the optimal timing for accurately estimating yield. Furthermore, this study aims to employ photographic quantification to measure the characteristics of corn ears and establish their correlation with corn grain yield. Ten corn hybrids were evaluated in a Complete Randomized Block (CRB) design with three replications across three locations. Vegetation and green leaf area indices were estimated throughout the growing cycle using an unmanned aerial vehicle (UAV) and were subsequently correlated with grain yield. The experiments consistently exhibited high levels of experimental quality across different locations, characterized by both high accuracy and low coefficients of variation. The experimental quality was consistently significant across all sites, with accuracy ranging from 79.07% to 95.94%. UAV flights conducted at the beginning of the crop cycle revealed a positive correlation between grain yield and the evaluated vegetation indices. However, a positive correlation with yield was observed at the V5 vegetative growth stage in Lavras and Ijaci, as well as at the V8 stage in Nazareno. In terms of corn ear phenotyping, the regression coefficients for ear width, length, and total number of grains (TNG) were 0.92, 0.88, and 0.62, respectively, demonstrating a strong association with manual measurements. The use of imaging for ear phenotyping is promising as a method for measuring corn components. It also enables the identification of the optimal timing to accurately estimate corn grain yield, leading to advancements in the agricultural imaging sector by streamlining the process of estimating corn production. [ABSTRACT FROM AUTHOR]

Amid a rapidly growing global population and increasing threats to crop yields, this review focuses on Speed Breeding (SB) in crop genetics. It traces SB's development from carbon arc lamp experiments 150 years ago to its modern use with LED technology which significantly accelerates breeding cycles. SB has applications in genetic mapping, genetic modification, and trait stacking, enhancing crop resilience by leveraging allelic diversity. It aligns well with breeding methods like single plant selection and single seed descent. The integration of SB with gene editing, genotyping, and genomic selection holds great promise. However, SB faces challenges related to infrastructure, genotypic variations, and potential stress responses. In summary, SB is a powerful and promising approach to address food security concerns and advancing crop genetics. [ABSTRACT FROM AUTHOR]

Background: The performance of oat genotypes differs across environments due to variations in biotic and abiotic factors. Thus, evaluation of oat genotypes across diverse environments is very important to identify superior and stable genotypes for yield improvement. Methods: The study aimed to assess the interaction (genotype‐by‐environment interaction; GEI) effect and determine the stability of grain yield in oat (Avena sativa L.) genotypes in Ethiopia using parametric and nonparametric stability statistics. Twenty‐four oat genotypes were evaluated in nine environments using a randomized complete block design replicated three times. Results: The pooled analysis of the variance of grain yield showed significant variations among genotypes, environments, and their interaction effects. Significant GEI revealed the rank order change of genotypes across environments. The environment main effect captured 44.62% of the total grain yield variance, while genotype and GEI effects explained 28.84% and 26.54% of the total grain yield variance, respectively. The grain yield stability was assessed based on 12 parametric and two nonparametric stability statistics. The results indicated that genotypes with superior grain yield‐ showed stable performance on the basis of the stability parameters of the genotypic superiority index (Pi), the Perkins and Jinks adjusted linear regression coefficient (Bi), and the yield stability index (YSI), indicating that selection using these stability parameters would be efficient for grain yield enhancement in oat genotypes. Spearman's rank correlation coefficients also showed that the stability parameters of Pi, Bi, and YSI had a significant positive association with grain yield. However, grain yield had an inverse correlation with the stability parameters of standard deviation, deviation from regression (Sdi2), the Hernandez desirability index (Dji), Wricke ecovalence (Wi), the Shukla stability variance (σi2), the AMMI stability value (ASV), and environmental variance (S(2)i), indicating that oat genotype selection using these stability parameters would not be efficient for yield enhancement because these stability parameters favor low‐yielding genotypes more, compared to high‐yielding ones. Conclusions: Therefore, G5, G8, G11, G12, G14, G16, G17, G19, and G22 genotypes were adaptable in all nine environments based on stability parameters of Pi, Bi, and YSI, and selection of these superior genotypes would improve grain yield in oat genotypes. However, the validity of this result should be confirmed by repeating the experiment in the same environments over two or more years. [ABSTRACT FROM AUTHOR]

Genetic variability is critical in order to create candidates for new superior varieties. This research objective was to evaluate the performance and variability of agronomical traits on the mungbean SSD on F4 V422H/129 population. The research was conducted at IPB University, Bogor, from March to June 2021. The SSD on F4 VR422H/129 population (378 genotypes with single plant as a representative of one genotype) and five check varieties were evaluated. The treatments were arranged in augmented design for RCBD in three replications. For agronomical traits, every F4 plant and 10 sample plants for each check variety were observed. Statistical analysis includes mean, frequency-distribution, heritability, genetic variability, correlation. The days to flowering, days to harvesting, generative periods, plant height on F4 V422H/129 were not significantly different from Vima 5, while total pod number, total pod weight, total seed weight, pod length were significantly higher. The agronomical traits were affected by genetic factors (heritability 0.71-0.99%), except for days to harvest. Based on the high genetic variability (CGV 0.62-0.64%), it was possible to select of total pod weight, total seed weight, or pod length in the next generation V422H/129. The total seed weight had a significant positive correlation with total pod weight and pod length. [ABSTRACT FROM AUTHOR]

Cowpea is the most important food legume in West and Central Africa and a valuable economic commodity in the region. Among the major biotic constraints to cowpea production are root parasitic weeds of which Alectra vogelii (Benth.) is of increasing importance. The cowpea landrace B301 was previously identified as a source of Alectra resistance, but neither the genes nor genomic loci conferring this resistance have been mapped. Therefore, to map and identify genetic markers linked to Alectra resistance for use in the molecular improvement of cowpea, we developed an F2 population from a cross of the susceptible variety 524B with B301. The population was phenotyped for resistance to A. vogelii and genotyped with a cowpea high density single nucleotide polymorphism (SNP) microarray. Putative resistance loci were mapped in F2 populations by categorical trait–multiple interval mapping and validated by selective genotyping. Selective genotyping indicated that the resistance loci on Vu04 (Rav1) and Vu11 (Rav2) were significantly associated with resistance (p ≤ 0.01). Using marker assisted backcrossing, the two resistance loci were introgressed independently into the susceptible 524B genetic background. Phenotyping and genotyping of the segregating backcross families delineated Rav1 to a 10 cM on chromosome 4 and Rav2 to a 6.7 cM interval in chromosome 11. These two loci are desirable for breeding Alectra resistant cowpea varieties due to their simple inheritance and ability to independently confer complete immunity to the parasite. [ABSTRACT FROM AUTHOR]

Accounts of twentieth-century agricultural industrialization in the United States and beyond often center the production and distribution of commercial F1 hybrid seeds as a pivotal development. The commercialization of hybrid corn seeds in the 1930s was initially heralded as a science-driven advance in agricultural productivity. However, since the 1970s "hybrid seeds" have been linked to many perceived perils attendant on industrialized agriculture, from the undermining of farmers' independence to the diminishment of crop genetic diversity to the consolidation of corporate control over the global food system. First grouped with the semidwarf varieties of the Green Revolution to emblematize capital- and chemical-intensive agriculture, hybrids are today often lumped together with genetically modified varieties for much the same reason. This essay revisits the scholarship that helped produce this understanding of hybrid seeds. It explores how and why the singular history of hybrid corn inflected understandings of crop breeding and seed production in general, contributing to lasting confusion about the promises and pitfalls of distinct approaches to crop development and the nature of hybrid seeds. [ABSTRACT FROM AUTHOR]

Rice is one of the most consumed cereals in the world and of extreme social and economic importance in Brazil. Minas Gerais is the leading State in irrigated rice production in the Southeast Region. This study aimed to estimate the genetic progress of 26 years of the irrigated rice breeding programme of Epamig in Southeast Brazil by time meta‐analysis. Genetic progress was estimated for grain yield, plant height and days to flowering. The dataset understood 162 genotypes in 91 trials of value for cultivation and use of 26 seasons. The rate of annual genetic gain for grain yield was estimated.99% (49.85 kg year−1). It was also verified that was a reduction in plant height and an increase in days to flowering, even if very low. Due to distinct historical phases of the rice breeding programme, there were changes in research focus and, consequently, affected the genetic gains. With this study, it was possible to evaluate the selection strategies carried out in the past and identify important points to maintain. [ABSTRACT FROM AUTHOR]

Plants remove carbon dioxide from the atmosphere through photosynthesis. Because agriculture's productivity is based on this process, a combination of technologies to reduce emissions and enhance soil carbon storage can allow this sector to achieve net negative emissions while maintaining high productivity. Unfortunately, current row-crop agricultural practice generates about 5% of greenhouse gas emissions in the United States and European Union. To reduce these emissions, significant effort has been focused on changing farm management practices to maximize soil carbon. In contrast, the potential to reduce emissions has largely been neglected. Through a combination of innovations in digital agriculture, crop and microbial genetics, and electrification, we estimate that a 71% (1,744 kg CO2e/ha) reduction in greenhouse gas emissions from row crop agriculture is possible within the next 15 y. Importantly, emission reduction can lower the barrier to broad adoption by proceeding through multiple stages with meaningful improvements that gradually facilitate the transition to net negative practices. Emerging voluntary and regulatory ecosystems services markets will incentivize progress along this transition pathway and guide public and private investments toward technology development. In the difficult quest for net negative emissions, all tools, including emission reduction and soil carbon storage, must be developed to allow agriculture to maintain its critical societal function of provisioning society while, at the same time, generating environmental benefits. [ABSTRACT FROM AUTHOR]

The agricultural sector is a significant contributor to greenhouse gas emissions, primarily through the release of carbon dioxide (CO 2), methane (CH 4), and nitrous oxide (N 2 O). These emissions are a major driver of climate change and pose a threat to global food security. This review examines the carbon footprint of agriculture, highlighting the connection between this sector and greenhouse gas emissions worldwide as well as the favourable interaction between food systems and climate change. This study investigates the causes and effects of the food chain to highlight the urgent need to develop novel agricultural methods. Precision farming, vertical farming, organic farming, and carbon-sequestering farms are a few of the innovative methods being addressed. Each has the potential to lower emissions and mitigate climate change. In the field of contemporary technologies, this review looks into improvements in crop genetics directed towards climate resilience and the use of carbon capture and utilization methods in agriculture. By increasing both sustainability and production, these advances have the potential to completely alter the agricultural environment. To build a sustainable food system that reduces carbon emissions and combats climate change while maintaining the food security of future generations, we emphasize the urgency of implementing these innovative technologies and practices. [Display omitted] • Sources and impacts of carbon emissions in agricultural field were provided. • Innovative farming practices such as organic farming and precision farming were focussed. • The importance of recent technological advancements in agriculture has been discussed. • Future perspectives on sustainability approaches were reviewed. [ABSTRACT FROM AUTHOR]

Genetic erosion can result in the loss of sorghum landrace genetic diversity. In the study areas, although it is generally believed that genetic erosion had occurred, there are no data on its amount and extent. Thus, this study is aimed to assess farmers' perception about the use of sorghum landraces and their genetic erosion and to identify suggested reasons for the replacement of sorghum landraces. To this end, a field survey of 1200 farmers, randomly selected over the three districts (Tenta, Mekdela, and Delanta) during 2006 to 2015/2016 main cropping seasons, was undertaken. Structured questionnaire survey of households, focused group discussions, key informant interviews, and field observations were used to collect data. Moreover, the data for samples collected during 1980 were obtained from the Ethiopian Biodiversity Institute (EBI). Sorghum landrace history profile analysis indicated that there was an insight in the use of local varieties among local farmers over the past three or above decades. However, there is a reduction trend due to the different selection criteria described by farmers. "Kokita," "Merar," "Marchuke," "Tinkish" (except for "Necho-Tinkish" and "Jofa-Tinkish"), and "Fesho" were totally excluded (lost) by local farmers attributed by home consumption preferences. The interviewed farmers indicated that genetic erosion had occurred. Genetic erosion of 100% was observed in white sorghum in Mekdela and 66.7% in Delanta and Tenta districts. Likewise, genetic erosion of red sorghum, 25%, 20%, and 75%, respectively, was detected in Tenta, Mekdela, and Delanta. For yellow sorghum grains, genetic erosion was 33.4% in Tenta and 66.7% in Mekdela and Delanta. Genetic erosion for "Tinkish" was found to be 66.7% in Tenta and 50% in Mekdela and Delanta. Based on farmer responses, genetic erosion was attributed to reduced benefits from landraces, drought, climate change, market price and demand, and reduction in land size. The actions of both natural and conscious selection on farm were also discussed in detail as genetic erosion scenarios. Therefore, attention should be given to conservation of farmers' varieties in which involving farmers' participation is very important in order to use their indigenous knowledge for conservation of FVs and on-farm conservation strategies should be practiced for FV sustainable use. Thus, genetic resource conservation is attained. [ABSTRACT FROM AUTHOR]

Genetic erosion can result in the loss of sorghum landrace genetic diversity. In the study areas, although it is generally believed that genetic erosion had occurred, there are no data on its amount and extent. Thus, this study is aimed to assess farmers' perception about the use of sorghum landraces and their genetic erosion and to identify suggested reasons for the replacement of sorghum landraces. To this end, a field survey of 1200 farmers, randomly selected over the three districts (Tenta, Mekdela, and Delanta) during 2006 to 2015/2016 main cropping seasons, was undertaken. Structured questionnaire survey of households, focused group discussions, key informant interviews, and field observations were used to collect data. Moreover, the data for samples collected during 1980 were obtained from the Ethiopian Biodiversity Institute (EBI). Sorghum landrace history profile analysis indicated that there was an insight in the use of local varieties among local farmers over the past three or above decades. However, there is a reduction trend due to the different selection criteria described by farmers. "Kokita," "Merar," "Marchuke," "Tinkish" (except for "Necho-Tinkish" and "Jofa-Tinkish"), and "Fesho" were totally excluded (lost) by local farmers attributed by home consumption preferences. The interviewed farmers indicated that genetic erosion had occurred. Genetic erosion of 100% was observed in white sorghum in Mekdela and 66.7% in Delanta and Tenta districts. Likewise, genetic erosion of red sorghum, 25%, 20%, and 75%, respectively, was detected in Tenta, Mekdela, and Delanta. For yellow sorghum grains, genetic erosion was 33.4% in Tenta and 66.7% in Mekdela and Delanta. Genetic erosion for "Tinkish" was found to be 66.7% in Tenta and 50% in Mekdela and Delanta. Based on farmer responses, genetic erosion was attributed to reduced benefits from landraces, drought, climate change, market price and demand, and reduction in land size. The actions of both natural and conscious selection on farm were also discussed in detail as genetic erosion scenarios. Therefore, attention should be given to conservation of farmers' varieties in which involving farmers' participation is very important in order to use their indigenous knowledge for conservation of FVs and on-farm conservation strategies should be practiced for FV sustainable use. Thus, genetic resource conservation is attained. [ABSTRACT FROM AUTHOR]

Societal Impact Statement: Hazelnut is consumed worldwide and is of critical economic importance to the rural communities of Turkey's northern coast. A new disease outbreak has drastically decreased yields across Turkey and climate change is emerging as a new threat to cultivation. Our study is the first to provide a genomic perspective on diversity in this vulnerable crop, which will prove valuable for future breeding efforts. Such research into perennial crops like hazelnut can help to improve farmer livelihoods and ensure the sustainability of crop production in a changing world. SummaryAssessing and describing genetic diversity in crop plants is a crucial first step toward their improvement. The European hazelnut, Corylus avellana L., is one of the most economically important tree nut crops worldwide. It is primarily produced in Turkey where rural communities depend on it for their livelihoods. Despite this, we know little about its domestication history and the genetic diversity it holds.We use double digest restriction‐site associated DNA (ddRAD) sequencing to produce a genome‐wide dataset containing wild and domesticated hazelnut. We uncover patterns of population structure and diversity, determine levels of crop‐wild gene flow, and estimate the relationships among different genetic clusters.We use a dataset of over 60k single nucleotide polymorphisms to find that genetic clusters of cultivars do not reflect their given names and that there is limited evidence for a reduction in genetic diversity in domesticated individuals. We find evidence that hazelnut may have been domesticated more than once and that admixture has likely occurred multiple times between wild and domesticated hazelnut.We provide the first genomic assessment of Turkish hazelnut diversity and suggest that there has not been an extreme bottleneck during the domestication of this crop, leading to cultivars at different stages of domestication. Our study provides a platform for further research that will protect hazelnut from the threats of climate change and an emerging fungal disease. [ABSTRACT FROM AUTHOR]

Simple sequence repeat (SSR) markers are powerful tools for the determination of relationships between genotypes and genetic diversity because of advantages such as high polymorphism, codominance nature, multiallelism and distribution on encoding and non-encoding regions, This study investigated the transferability and polymorphism of 102 barley SSR markers in 41 bread and durum wheat and triticale genotypes. A total of 50 pair primers were transferable, and 40 pair primers producing 118 alleles (on average 2.95 alleles per locus) were polymorphic. The Polymorphism Information Content and genetic diversity for these markers were estimated to be 29% and 33%, respectively. The average of Shannon and Nei indices for the studied genotypes were 34% and 23%, respectively. Cluster analysis, using a Minimum Evolution algorithm and P-distance coefficient, assigned the genotypes into five groups. In principal coordinates analysis, the first principal component explained 74.69% of the total molecular variation. Analysis of molecular variance based on the genome structure of the genotypes using molecular data revealed a high level of variation within groups. In conclusion, this study has identified a set of 50 polymorphic SSR markers of barley as being useful for diversity analysis of common wheat, durum wheat, and triticale. These microsatellites could be used for diversity analysis, molecular mapping/QTL analysis, molecular marker-assisted selection, and comparative genome analysis. [ABSTRACT FROM AUTHOR]

Clustered regularly interspaced short palindromic repeats (CRISPR)‐based genome editing, derived from prokaryotic immunity system, is rapidly emerging as an alternative platform for introducing targeted alterations in genomes. The CRISPR‐based tools have been deployed for several other applications including gene expression studies, detection of mutation patterns in genomes, epigenetic regulation, chromatin imaging, etc. Unlike the traditional genetic engineering approaches, it is simple, cost‐effective, and highly specific in inducing genetic variations. Despite its popularity, the technology has limitations such as off‐targets, low mutagenesis efficiency, and its dependency on in‐vitro regeneration protocols for the recovery of stable plant lines. Several other issues such as persisted CRISPR activity in subsequent generations, the potential for transferring to its wild type population, the risk of reversion of edited version to its original phenotype particularly in cross‐pollinated plant species when released into the environment and the scarcity of validated targets have been overlooked. This article briefly highlights these undermined aspects, which may challenge the wider applications of this platform for improving crop genetics. [ABSTRACT FROM AUTHOR]

Background: Triticum aestivum (wheat) is one of the world's oldest crops and has been used for >8000 years as a food crop in North Africa, West Asia and Europe. Today, wheat is one of the most important sources of grain for humans, and is cultivated on greater areas of land than any other crop. As the human population increases and soil salinity becomes more prevalent, there is increased pressure on wheat breeders to develop salt-tolerant varieties in order to meet growing demands for yield and grain quality. Here we developed a mutant wheat population using the moderately salt-tolerant Bangladeshi variety BARI Gom-25, with the primary goal of further increasing salt tolerance. Results: After titrating the optimal ethyl methanesulfonate (EMS) concentration, ca 30,000 seeds were treated with 1% EMS, and 1676 lines, all originating from single seeds, survived through the first four generations. Most mutagenized lines showed a similar phenotype to BARI Gom-25, although visual differences such as dwarfing, giant plants, early and late flowering and altered leaf morphology were seen in some lines. By developing an assay for salt tolerance, and by screening the mutagenized population, we identified 70 lines exhibiting increased salt tolerance. The selected lines typically showed a 70% germination rate on filter paper soaked in 200 mM NaCl, compared to 0–30% for BARI Gom-25. From two of the salt-tolerant OlsAro lines (OA42 and OA70), genomic DNA was sequenced to 15x times coverage. A comparative analysis against the BARI Gom-25 genomic sequence identified a total of 683,201 (OA42), and 768,954 (OA70) SNPs distributed throughout the three sub-genomes (A, B and D). The mutation frequency was determined to be approximately one per 20,000 bp. All the 70 selected salt-tolerant lines were tested for root growth in the laboratory, and under saline field conditions in Bangladesh. The results showed that all the lines selected for tolerance showed a better salt tolerance phenotype than both BARI Gom-25 and other local wheat varieties tested. Conclusion: The mutant wheat population developed here will be a valuable resource in the development of novel salt-tolerant varieties for the benefit of saline farming. [ABSTRACT FROM AUTHOR]

The implications of freezing seeds to conserve genes statically and for the long term are complex and deserve further reflection to appreciate seed banking as an attempt to detach seeds from their life cycle. Here, I use a cryopolitical framework to explore this in the context of the activities of the International Board of Plant Genetic Resources (IBPGR) between 1973 and 1984. I suggest that the emergence of seed banks is a shift toward a cryopower mode of governance, where technoscientific intervention in the biology of seeds was presented as a means to manage the survival of seeds. The project of ex situ conservation is a socio‐technical effort by international institutions such as IBPGR and a variety of institutions with seed repositories. In creating a coldscape, they sought to make genetic resources into frozen seeds that were stable and mobile, not only across space but, importantly, over time. Consequently, our interpretations of seed banks as sites of geopolitical significance in the controversies over access to seeds can be complemented by considering their biopolitical importance as interventions that extend the power of IBPGR and other institutions toward plant life, and the future. [ABSTRACT FROM AUTHOR]

The Mediterranean sesame core collection contains agro-morphologically superior sesame accessions from geographically diverse regions in four continents. In the present investigation, the genetic diversity and population structure of this collection was analyzed with 5292 high-quality SNPs discovered by double-digest restriction site associated DNA (ddRAD) sequencing, a cost-effective and flexible next-generation sequencing method. The genetic distance between pairs of accessions varied from 0.023 to 0.524. The gene diversity was higher in accessions from Asia than from America, Africa, and Europe. The highest genetic differentiation was observed between accessions collected from America and Europe. Structure analysis showed the presence of three subpopulations among the sesame accessions, and only six accessions were placed in an admixture group. Phylogenetic tree and principal coordinate analysis clustered the accessions based on their countries of origin. However, no clear division was evident among the sesame accessions with regard to their continental locations. This result was supported by an AMOVA analysis, which revealed a genetic variation among continental groups of 5.53% of the total variation. The large number of SNPs clearly indicated that the Mediterranean sesame core collection is a highly diverse genetic resource. The collection can be exploited by breeders to select appropriate accessions that will provide high genetic gain in sesame improvement programs. The high-quality SNP data generated here should also be used in genome-wide association studies to explore qualitative trait loci and SNPs related to economically and agronomically important traits in sesame. [ABSTRACT FROM AUTHOR]

Classical crop models have been developed to predict crop yield and quality, and they are based on physiological and environmental inputs. After molecular discoveries, models should integrate genetic variation to allow predictions that are more genotype-dependent. An interesting approach, Quantitative Trait Locus (QTL)-based ecophysiological modeling, has shown promising results for the design of ideotypes that are adapted to biotic and abiotic stresses, but there are still limitations to attaining a fully integrated model. The aim of this case study is to clarify the impact of choosing different model equations (closely related and with different numbers of parameters) and optimization methods on the detection of QTLs controlling the parameters of crop growth. Different growth equations were parameterized based on a genetic population by following different approaches. The correlations between parameters were analyzed, and two different strategies were adopted to address the correlation issue. QTL analysis was performed on the optimized values of the parameters of the growth equations and on the observed dry mass (DM) data to validate the QTLs detected. Overall, models and strategies resulted in different QTLs being detected. Similar LOD profiles but with peaks of different heights were observed, some of which were significant, resulting in different numbers of QTLs. In some cases, peaks had slightly different positions or were absent. Even closely related growth models led to the detection of different QTLs. The goodness of fit and complexity of the growth models were found to be insufficient to select the best model. Calculating parameters independently of observed data may not be a good strategy, whereas setting parameters independent of the genotype is recommended. Given the large-scale global optimization problem and the strong correlations between parameters, the two algorithms tested showed poor performance. Currently, the lack of effective algorithms is the main obstacle to answering the question posed. The authors therefore suggest testing different model formulations and comparing the QTLs detected before choosing the best formulation to use in an ecophysiological modeling approach based on QTLs. [ABSTRACT FROM AUTHOR]

The objective of this study was to evaluate the effects of additive and non-additive genes on the efficiency of nitrogen (N) use and N responsiveness in inbred popcorn lines. The parents, hybrids and reciprocal crosses were evaluated in a 10x10 triple lattice design at two sites and two levels of N availability. To establish different N levels in the two experiments, fertilization was carried out at sowing, according to soil analysis reports. However, for the experiments with ideal nitrogen availability, N was sidedressed according to the crop requirement, whereas for the N-poor experiments sidedressing consisted of 30% of that applied in the N-rich environment. Two indices were evaluated, the Harmonic Mean of the Relative Performance (HMRP) and Agronomic Efficiency under Low Nitrogen Availability (AELN), both based on grain yield at both N levels. Both additive and non-additive gene effects were important for selection for N-use efficiency. Moreover, there was allelic complementarity between the lines and a reciprocal effect for N-use efficiency, indicating the importance of the choice of the parents used as male or female. The best hybrids were obtained from inbred popcorn lines with contrasting N-use efficiency and N responsiveness. [ABSTRACT FROM AUTHOR]

Summary: Broadening the genetic base of crops is crucial for developing varieties to respond to global agricultural challenges such as climate change. Here, we analysed a diverse panel of 371 domesticated lines of the model crop barley to explore the genetics of crop adaptation. We first collected exome sequence data and phenotypes of key life history traits from contrasting multi‐environment common garden trials. Then we applied refined statistical methods, including some based on exomic haplotype states, for genotype‐by‐environment (G×E) modelling. Sub‐populations defined from exomic profiles were coincident with barley's biology, geography and history, and explained a high proportion of trial phenotypic variance. Clear G×E interactions indicated adaptation profiles that varied for landraces and cultivars. Exploration of circadian clock‐related genes, associated with the environmentally adaptive days to heading trait (crucial for the crop's spread from the Fertile Crescent), illustrated complexities in G×E effect directions, and the importance of latitudinally based genic context in the expression of large‐effect alleles. Our analysis supports a gene‐level scientific understanding of crop adaption and leads to practical opportunities for crop improvement, allowing the prioritisation of genomic regions and particular sets of lines for breeding efforts seeking to cope with climate change and other stresses. Significance Statement: We analysed exome sequence data and life history traits measured in multi‐environment trials of a diverse panel of 371 domesticated barley lines to explore the genetics of crop adaptation. G×E interactions indicated adaptation profiles that varied for sub‐populations defined from exomic data. Exploration of circadian clock‐related genes associated with days to heading revealed complexities in G×E effect directions, and the importance of latitudinally based genic context in the expression of large effect alleles. Analysis provides practical information for future crop breeding. [ABSTRACT FROM AUTHOR]

Volatile profiles of oat‐based foods are mainly analyzed on the oat flakes and porridge as snack or breakfast, whereas the volatile characteristics of the traditional Chinese oat meal (TCOM), a popular main food in some regions of northern China, with special strong aroma, are not known. Here, we compared the volatile profiles from headspace solid phase microextraction gas chromatography–mass spectrometry analysis of oat porridge (OP) and TCOM, which were of different processing and cooking methods, from those of different cultivars, and analyzed the effect of cultivation locations on oat volatile features. Apart from the 35 volatiles shared by OP and TCOM, there were 23 and 24 volatiles specific to OP and TCOM, respectively, with the later showing more toasting and frying‐related volatiles due to the dry frying process of the grains before milling. Principle component analysis of the volatiles of OP and TCOM from 16 cultivars showed that they were clustered into two groups, and four cultivars were clustered together, independent of processing and cooking methods. The oat volatile profiles of cultivars grown in three regions of north China were dependent on the cultivation locations rather than cultivars, regardless of OP or TCOM, with those from Datong of Shanxi Province and Zhangjiakou of Hebei Province clustered together. The location effect could be due to significant less precipitation in the two regions above than the other region Ulanqab of Inner Mongolia. Practical Application: The volatile compounds in oat are closely related to cultivation regions, which could be applied as a key factor by oat producers for marketing. The four cultivars showed similar and stable volatile profiles, which could be used as reference cultivars for breeding of high‐quality oat with better flavor. [ABSTRACT FROM AUTHOR]

In Brassica oleracea, heterosis is the most efficient tool providing impetus to hybrid vegetable industry. In this context, we presented the first report on identifying superior heterotic crosses for yield and commercial traits in cauliflower involving cytoplasmic male sterile (CMS) and doubled haploid (DH) lines as parents. We studied the suitability of genomic-SSRs and EST-SSRs based genetic distance (GD) and agronomic trait based phenotypic distance (PD) for predicting heterosis in F1 hybrids using CMS and DH based parents. 120 F1 hybrids derived from 20Ogura based CMS lines and 6 DH based testers were evaluated for 16 agronomic traits along with the 26 parental lines and 4 commercial standard checks. The genomic-SSRs and EST-SSRs based genetic structure analysis grouped the 26 parental lines into 4 distinct clusters. The CMS lines Ogu118-6A, Ogu33A, Ogu34-1A were good general combiner for developing early maturity hybrids. The SCA effects were significantly associated with heterosis suggesting non-additive gene effects for the heterotic response of hybrids. Less than unity value of σ2A/D coupled with σ2gca/σ2sca indicated the predominance of non-additive gene action in the expression of studied traits. The correlation analysis of genetic distance with heterosis for commercial traits suggested that microsatellites based genetic distance estimates can be helpful in heterosis prediction to some extent. [ABSTRACT FROM AUTHOR]

A multi-trait selective breeding program of Macrobrachium rosenbergii was initiated in China in 2015. In this program, the M. rosenbergii resources were widely collected from four countries, the origin of the founders was verified with 16 microsatellites and the pedigree was reconstructed, and the optimum contribution selection was used to make the mating design. In this study, we evaluated the genetic parameters and selection response for the harvest body weight (HBW) of M. rosenbergii after being communally reared for 95–109 days. The data were collected from two generations that comprised 25,212 progenies from 150 sires and 198 dams. The residual maximum-likelihood methodology was employed to evaluate the variance components, by fitting an animal model. The accuracy of estimated breeding values increased by 0.38% after pedigree reconstruction using microsatellite markers. The estimated heritability (h2) for HBW was moderate (0.212 ± 0.049) and the common environmental coefficient (c2) was low (0.063 ± 0.017) when all the data were used for the analysis. Within generations, h2 was moderate to high (0.198 ± 0.080 to 0.338 ± 0.049). c2 could only be estimated in G1, which was 0.055 ± 0.030. The average HBW of males was significantly larger than that of females (P < 0.01). h2 estimated for female HBWs were higher than that for males within generations, while h2 estimated for female HBWs were lower than that for males across generations. But they were not significantly different (P > 0.05). The genetic correlations between sexes were moderate to high within each generation (0.529 to 0.763). Two methods were used to estimate the realized response. One method was calculated from the differences between the least squares means of the selected population HBW and that of control population HBW, which was 14.01%. The other method was calculated from the differences between the EBVs of the selected population HBW and that of control population HBW, which was 11.52%. The predicted responses derived from two sets of genetic parameters acquired from within- and across- generation datasets were 11.68% and 10.67%, respectively. The present study provides valuable information for breeding programs of M. rosenbergii. [ABSTRACT FROM AUTHOR]

Summary: Maize (Zea mays) has multiple uses in human food, animal fodder, starch and sweetener production and as a biofuel, and is accordingly the most extensively cultivated cereal worldwide. To enhance maize production, genetic factors underlying important agricultural traits, including stress tolerance and flowering, have been explored through forward and reverse genetics approaches. Co‐functional gene networks are systems biology resources useful in identifying trait‐associated genes in plants by prioritizing candidate genes. Here, we present MaizeNet (http://www.inetbio.org/maizenet/), a genome‐scale co‐functional network of Z. mays genes, and a companion web server for network‐assisted systems genetics. We describe the validation of MaizeNet network quality and its ability to functionally predict molecular pathways and complex traits in maize. Furthermore, we demonstrate that MaizeNet‐based prioritization of candidate genes can facilitate the identification of cell wall biosynthesis genes and detect network communities associated with flowering‐time candidate genes derived from genome‐wide association studies. The demonstrated gene prioritization and subnetwork analysis can be conducted by simply submitting maize gene models based on the commonly used B73 RefGen_v3 and the latest B73 RefGen_v4 reference genomes on the MaizeNet web server. MaizeNet‐based network‐assisted systems genetics will substantially accelerate the discovery of trait‐associated genes for crop improvement. Significance Statement: In this report, we describe MaizeNet, a functional gene network for Zea mays, the most extensively produced cereal worldwide, and demonstrate its ability to predict genes for complex traits such as cell wall biosynthesis and flowering time. Along with web‐based tools for gene prioritization and subnetwork analysis, MaizeNet will facilitate the discovery of trait‐associated genes for crop improvement. [ABSTRACT FROM AUTHOR]

Sugarcane (Saccharum spp.) has a complex genome with variable ploidy and frequent aneuploidy, which hampers the understanding of phenotype and genotype relations. Despite this complexity, genome-wide association studies (GWAS) may be used to identify favorable alleles for target traits in core collections and then assist breeders in better managing crosses and selecting superior genotypes in breeding populations. Therefore, in the present study, we used a diversity panel of sugarcane, called the Brazilian Panel of Sugarcane Genotypes (BPSG), with the following objectives: (i) estimate, through a mixed model, the adjusted means and genetic parameters of the five yield traits evaluated over two harvest years; (ii) detect population structure, linkage disequilibrium (LD) and genetic diversity using simple sequence repeat (SSR) markers; (iii) perform GWAS analysis to identify marker-trait associations (MTAs); and iv) annotate the sequences giving rise to SSR markers that had fragments associated with target traits to search for putative candidate genes. The phenotypic data analysis showed that the broad-sense heritability values were above 0.48 and 0.49 for the first and second harvests, respectively. The set of 100 SSR markers produced 1,483 fragments, of which 99.5% were polymorphic. These SSR fragments were useful to estimate the most likely number of subpopulations, found to be four, and the LD in BPSG, which was stronger in the first 15 cM and present to a large extension (65 cM). Genetic diversity analysis showed that, in general, the clustering of accessions within the subpopulations was in accordance with the pedigree information. GWAS performed through a multilocus mixed model revealed 23 MTAs, six, three, seven, four and three for soluble solid content, stalk height, stalk number, stalk weight and cane yield traits, respectively. These MTAs may be validated in other populations to support sugarcane breeding programs with introgression of favorable alleles and marker-assisted selection. [ABSTRACT FROM AUTHOR]

Assessment of genetic diversity and population structure in crops is essential for breeding and germplasm conservation. A collection of 354 bread wheat genotypes, including Mediterranean landraces and modern cultivars representative of the ones most widely grown in the Mediterranean Basin, were characterized with 11196 single nucleotide polymorphism (SNP) markers. Total genetic diversity (HT) and polymorphic information content (PIC) were 0.36 and 0.30 respectively for both landraces and modern cultivars. Linkage disequilibrium for the modern cultivars was higher than for the landraces (0.18 and 0.12, respectively). Analysis of the genetic structure showed a clear geographical pattern for the landraces, which were clustered into three subpopulations (SPs) representing the western, northern and eastern Mediterranean, whereas the modern cultivars were structured according to the breeding programmes that developed them: CIMMYT/ICARDA, France/Italy, and Balkan/eastern European countries. The modern cultivars showed higher genetic differentiation (GST) and lower gene flow (0.1673 and 2.49, respectively) than the landraces (0.1198 and 3.67, respectively), indicating a better distinction between subpopulations. The maximum gene flow was observed between landraces from the northern Mediterranean SPs and the modern cultivars released mainly by French and Italian breeding programmes. [ABSTRACT FROM AUTHOR]

Castor bean is an important seed oil crop. Castor oil is a highly demanded oil for several industrial uses. Currently, castor bean varieties suffer from low productivity and high risk of insect pests and diseases. It is in urgent need to mine elite genes from wild materials for castor breeding. 29 pairs of polymorphic SRAP primers out of 361 pairs were used to analyse the genetic diversity of 473 wild castor materials from South China. 203 bands were amplified by the 29 pairs of primers, of which 169 bands were polymorphic, with a polymorphic percentage of 83.25%. With an average number of alleles per locus (Ap) of 1.801, average number of effective alleles per locus (Ae) of 1.713 and average percentage of polymorphic loci (P) of 90.04%, these primers were proven to be useful and effective. Nei’ genetic distance between the materials ranged from 1.04 to 25.02, with an average of 13.03. At the genetic distance of 25.02, the materials clustered into two major groups, consistent with the result of population structure analysis. However, more subgroups existed between 5.21 and 13.32. Although not all the materials from the same region were clustered in the same group, an obvious trend existed where the groups were related to regions to a great extent. Based on multiple indices, the genetic diversity of materials from Hainan was the lowest. However, there was not much difference between West Guangdong and Guangxi, although the former was slightly higher. Moderate genetic differentiation was observed in wild materials in South China. The genetic differentiation mainly occurred within population, with maximum differentiation in Guangxi, followed by West Guangdong and the minimum in Hainan. Nonetheless, there was an extensive geneflow between populations. The above results provided a direction for the conservation and breeding application of these materials. [ABSTRACT FROM AUTHOR]

Pigeonpea is a major source of dietary protein to the vegetarian population of the Indian sub-continent. Crop improvement to mitigate biotic and abiotic stresses for realization of its potential yield and bridging yield gap is the need of the hour. Availability of limited genomic resources in the cultivated germplasm, however, is a serious bottleneck towards successful molecular breeding for the development of superior genotypes in pigeonpea. In view of this, improvement of pigeonpea can be attempted through transgenesis or by exploiting genetic resources from its wild relatives. Pigeonpea wild relatives are known to be bestowed with agronomic traits of importance; discovery and deployment of genes from them can provide a lucrative option for crop improvement. Understanding molecular signatures of wild relatives would not only provide information about the mechanism behind desired traits but also enable us to extrapolate the information to cultivated pigeonpea. The present study deals with the characterization of leaf transcriptomes of Cajanus cajan and one of its wild relatives, Cajanus platycarpus. Illumina sequencing revealed 0.11 million transcripts in both the species with an annotation of 0.09 million (82%) transcripts using BLASTX. Comparative transcriptome analyses on the whole, divulged cues about the wild relative being vigilant and agile. Gene ontology and Mapman analysis depicted higher number of transcripts in the wild relative pertaining to signaling, transcription factors and stress responsive genes. Further, networking between the differentially expressed MapMan bins demonstrated conspicuous interactions between different bins through 535 nodes (512 Genes and 23 Pathways) and 1857 edges. The authenticity of RNA-seq analysis was confirmed by qRT-PCR. The information emanating from this study can provide valuable information and resource for future translational research including genome editing to alleviate varied stresses. Further, this learning can be a platform for in-depth investigations to decipher molecular mechanisms for mitigation of various stresses in the wild relative. [ABSTRACT FROM AUTHOR]

Rhizomes of Atractylodes lancea are used in traditional Japanese medicine (Kampo) and Chinese medicine to treat numerous diseases and disorders because they contain many pharmacologically active compounds. The major active compounds in A. lancea are essential oil compounds such as β-eudesmol, hinesol, atractylon, and atractylodin. The contents of the compounds in A. lancea exhibit high variability depending on their habitat. We cultivated clonal lines of A. lancea in different years (2016, 2017) and different locations (Hokkaido, Ibaraki) to investigate the influence of genetic and environmental factors on the contents of major compounds, namely, β-eudesmol, hinesol, atractylon, and atractylodin. Broad sense heritability of β-eudesmol, hinesol, atractylon, and atractylodin contents were 0.84, 0.77, 0.86, and 0.87, respectively. The effects of interannual variability on the contents of the compounds were lower than those of genotype. In addition, the cultivated environmental factors were assessed by different locations, and the correlations between Hokkaido and Ibaraki grown plants based on β-eudesmol, hinesol, atractylon, and atractylodin contents were 0.94, 0.94, 1.00, and 0.83, respectively. The results suggest that the contents of β-eudesmol, hinesol, atractylon, and atractylodin in A. lancea are largely influenced by genetic factors, and clonal propagation could be an effective strategy for obtaining populations with high contents of essential oil compounds. Furthermore, the contents of β-eudesmol, hinesol, atractylon, and atractylodin in A. lancea exhibited few correlations with rhizome yields. A. lancea cultivars with not only high contents of essential oil compounds but also high rhizome yield could be developed through selective breeding. [ABSTRACT FROM AUTHOR]

Agricultural expansion and the need for sustainable cultivation are challenges faced by researchers involved in the generation of new cultivars that can adapt to abiotic stress. Knowledge of the genetic effects of characteristics related to efficiency and responsiveness to phosphorus use must be considered when implementing methods to obtain better genotypes. The aim of this study was to characterize and select popcorn hybrids based on their efficiency and responsiveness to phosphorus use, and estimate their combining abilities and genetic effects via diallel analysis to implement improvement programs for sustainable agriculture. Eight contrasting inbred lines were used to obtain simple hybrids for diallel analysis. Twenty-eight diallelic hybrids plus the popcorn parental lines were evaluated at two different sites under two contrasting environments for soil phosphorus availability (6 × 6 lattice design). Grain yield, popping expansion, and volume of expanded popcorn per hectare were measured. A combined analysis of variance and a test of means were performed. The classification and utilization of the phosphorus use efficiency index, according to the grain yield performance of the hybrids under contrasting environments, was considered. Through model 2 of the Griffing’s diallel analysis method, the general and specific combining abilities were estimated, along with their environmental interactions. The best strategy to obtain genotypes that are efficient and responsive to phosphorus involves exploring popcorn hybrids using genitors that result in the accumulation of additive genes that promote popping expansion. Hybrids P7 × L80, P7 × L59, P7 × L76, and P6 × L80 presented promising results and may be evaluated as cultivation options in phosphorus-deficient soils. [ABSTRACT FROM AUTHOR]

The present investigation was made to generate information on the heterotic pools amongst pearl millet hybrid parents. A set of 17 representative parents was selected from a diverse set of 147 hybrid parents using SSR based genetic distance (GD) and clustering pattern; 136 hybrids were developed in diallel fashion and evaluated at two locations in India. Moderate positive significant correlation (r = 0.37, p<0.01) and (r = 0.33, p<0.01) was found between GD and mid-parent heterosis (MPH) and better-parent heterosis (BPH), respectively, for grain yield for all the hybrids. Higher correlation between genetically closer individuals was observed for grain yield heterosis when the parents of B- and R- crosses had lesser genetic distance (<0.68 GD) in comparison to those parental combinations having GD higher than 0.68, indicating that the GD based predictions for grain yield are better when the parents are genetically related than when they are genetically diverse. In this study, all the pearl millet hybrid parents seems to exist in two broad-based heterotic pools; one each represented by seed and restorer parents as B × R hybrids showed highest mean heterosis for grain yield than either of B × B or R × R crosses. Further, four heterotic pools have been identified in this diverse set of hybrid parents of pearl millet, two each for seed parents (HPB1 and HPB2) and for restorer parents (HPR3 and HPR4). Among these, HPB1 × HPR3 was identified having the highest heterotic level, and could be further used to develop higher yielding pearl millet hybrids. [ABSTRACT FROM AUTHOR]

Brassica crops require high amounts of inorganic sulfur (S) for optimum yield, and are characterized by the synthesis of S-rich glucosinolates (GSL). Although it is well established that seed and GSL yield can be increased by S fertilizer, the detailed relationship between S supply as primary source and the harvestable sinks of seed GSL and storage proteins is poorly understood. We tested the hypothesis that Brassica juncea mustard seed acts as a secondary S sink, and so require a higher rate of S to achieve maximum seed GSL compared to rates required to attain maximum seed biomass. Our experimental strategy involved comparing responses to available S for seed biomass, GSL, and protein. This was carried out in a protected environment using sand culture for a high-GSL condiment-type homozygous B. juncea genotype. A low-GSL canola-type was used as a control, in order to establish a base-line of response. Significantly more S was required to achieve maximum seed GSL than was required to achieve maximum seed mass. Total seed protein content was not significantly affected by increased S. The high-GSL line appeared to have an efficient mechanism of S supply to the secondary S sink, given the observed increase in seed S with increased S availability. From a practical point of view, increases in seed GSL with S availability suggests that S fertilizer rates should be optimized for maximum seed GSL yield, rather that optimizing for seed yield, as occurs for most other crops. [ABSTRACT FROM AUTHOR]

Usage of high-throughput sequencing approaches allow for the generation and characterization of reference transcriptome datasets that support gene-based marker discovery, which in turn can be used to build genetic maps among other purposes. We have obtained a transcriptome assembly including 49,453 genes for the lentil (Lens culinaris Medik.) cultivar Alpo using RNAseq methodology. This transcriptome was used as reference to obtain 6,306 quality polymorphic markers (SNPs and short indels) analyzing genotype data from a RIL population at F7 generation derived from the interspecific cross between L. culinaris cv. Alpo and L. odemensis accession ILWL235. L. odemensis is a wild species included in the secondary gene pool and can be used as a source for gene introgression in lentil breeding programs. Marker data were used to construct the first genetic interspecific map between these two species. This linkage map has been used to precisely identify regions of the CDC-Redberry lentil draft genome in which the candidate genes for some qualitative traits (seed coat spotting pattern, flower color, and stem pigmentation) could be located. The genome regions corresponding to a significant single quantitative trait locus (QTL) controlling “time to flowering” located in chromosome 6 and three QTLs regulating seed size and positioned in chromosomes 1 and 5 (two QTLs) were also identified. Significant QTLs for Ascochyta blight resistance in lentil were mapped to chromosome 6 in the genome region or close to it where QTLs for Ascochyta blight resistance have previously been reported. [ABSTRACT FROM AUTHOR]

Chickpea is one of the most important food legumes that holds the key to meet rising global food and nutritional demand. In order to deploy molecular breeding approaches in crop improvement programs, user friendly and cost effective marker resources remain prerequisite. The advent of next generation sequencing (NGS) technology has resulted in the generation of several thousands of markers as part of several large scale genome sequencing and re-sequencing initiatives. Very recently, PCR based Insertion-deletions (InDels) are becoming a popular gel based genotyping solution because of their co-dominant, inexpensive, and highly polymorphic nature. With an objective to expand marker resources for genomics assisted breeding (GAB) in chickpea, whole genome re-sequencing data generated on five parental lines of one interspecific (ICC 4958 × PI 489777) and two intra-specific (ICC 283 × ICC 8261 and ICC 4958 × ICC 1882) mapping populations, were used for identification of InDels. A total of 231,658 InDels were identified using Dindel software with default parameters. Further, a total of 8,307 InDels with ≥20 bp size were selected for development of gel based markers, of which primers could be designed for 7,523 (90.56%) markers. On average, markers appeared at a frequency of 1,038 InDels/LG with a maximum number of markers on CaLG04 (1,952 InDels) and minimum on CaLG08 (360 InDels). In order to validate these InDels, a total of 423 primer pairs were randomly selected and tested on the selected parental lines. A high amplification rate of 80% was observed ranging from 46.06 to 58.01% polymorphism rate across parents on 3% agarose gel. This study clearly reflects the usefulness of available sequence data for the development of genome-wide InDels in chickpea that can further contribute and accelerate a wide range of genetic and molecular breeding activities in chickpea. [ABSTRACT FROM AUTHOR]

The concept of a pan-genome refers to intraspecific diversity in genome content and structure, encompassing both genes and intergenic space. Pan-genomic studies employ a combination of de novo sequence assembly and reference-based alignment to discover and genotype structural variants. The large size and complex structure of Triticeae genomes were for a long time an obstacle for genomic research in barley and its relatives. Now that a reference genome is available, computational pipelines for high-quality sequence assembly are in place, and sequence costs continue to drop, investigations into the structural diversity of the barley genome seem within reach. Here, we review the recent progress on pan-genomics in the model grass Brachypodium distachyon, and the cereal crops rice and maize, and devise a multi-tiered strategy for a pan-genome project in barley. Our design involves: (1) the construction of high-quality de novo sequence assemblies for a small core set of representative genotypes, (2) short-read sequencing of a large diversity panel of genebank accessions to medium coverage and (3) the use of complementary methods such as chromosome-conformation capture sequencing and k-mer-based association genetics. The in silico representation of the barley pan-genome may inform about the mechanisms of structural genome evolution in the Triticeae and supplement quantitative genetics models of crop performance for better accuracy and predictive ability. [ABSTRACT FROM AUTHOR]

The identification and isolation of genes underlying quantitative trait loci (QTLs) associated with agronomic traits in crops have been recently accelerated thanks to next-generation sequencing (NGS)-based technologies combined with plant genetics. With NGS, various revisited genetic approaches, which benefited from higher marker density, have been elaborated. These approaches improved resolution in QTL position and assisted in determining functional causative variations in genes. Examples of QTLs/genes associated with agronomic traits in crops and identified using different strategies based on whole-genome sequencing (WGS)/whole-genome resequencing (WGR) or RNA-seq are presented and discussed in this review. More specifically, we summarize and illustrate how NGS boosted bulk-segregant analysis (BSA), expression profiling, and the construction of polymorphism databases to facilitate the detection of QTLs and causative genes. Highlights The swift development of next-generation sequencing (NGS) has accelerated quantitative trait locus (QTL) mapping and gene discovery in crops. High-throughput NGS-based genotyping platforms provide an extensive capacity to develop comprehensive polymorphism datasets including SNPs, InDels, structural variations, and genomic rearrangement. Whole-genome resequencing combined with bulk-segregant analysis offers a high density of informative SNPs, helping to detect QTLs without genotyping the entire mapping population. However, phenotyping of the entire population is still required. RNA-seq is useful to simultaneously genotype and phenotype segregating populations, releasing genomic information on mRNA and expression levels. Polymorphism databases generated by whole-genome sequencing using large-accession collections constitute new shared resources that facilitate QTL detection and gene discovery. [ABSTRACT FROM AUTHOR]

Information on crop pedigrees can be used to help maximise genetic gain in crop breeding and allow efficient management of genetic resources. We present a pedigree resource of 2,657 wheat (Triticum aestivum L.) genotypes originating from 38 countries, representing more than a century of breeding and variety development. Visualisation of the pedigree enables illustration of the key developments in United Kingdom wheat breeding, highlights the wide genetic background of the UK wheat gene pool, and facilitates tracing the origin of beneficial alleles. A relatively high correlation between pedigree- and marker-based kinship coefficients was found, which validated the pedigree and enabled identification of errors in the pedigree or marker data. Using simulations with a combination of pedigree and genotype data, we found evidence for significant effects of selection by breeders. Within crosses, genotypes are often more closely related than expected by simulations to one of the parents, which indicates selection for favourable alleles during the breeding process. Selection across the pedigree was demonstrated on a subset of the pedigree in which 110 genotyped varieties released before the year 2000 were used to simulate the distribution of marker alleles of 45 genotyped varieties released after the year 2000, in the absence of selection. Allelic diversity in the 45 varieties was found to deviate significantly from the simulated distributions at a number of loci, indicating regions under selection over this period. The identification of one of these regions as coinciding with a strong yield component quantitative trait locus (QTL) highlights both the potential of the remaining loci as wheat breeding targets for further investigation, as well as the utility of this pedigree-based methodology to identify important breeding targets in other crops. Further evidence for selection was found as greater linkage disequilibrium (LD) for observed versus simulated genotypes within all chromosomes. This difference was greater at shorter genetic distances, indicating that breeder selections have conserved beneficial linkage blocks. Collectively, this work highlights the benefits of generating detailed pedigree resources for crop species. The wheat pedigree database developed here represents a valuable community resource and will be updated as new varieties are released at . [ABSTRACT FROM AUTHOR]

Safflower (Carthamus tinctorius L.) is a multipurpose crop of dry land yielding very high quality of edible oil. Present study was aimed to investigate the genetic diversity and population structure of 131 safflower accessions originating from 28 different countries using 13 iPBS-retrotransposon markers. A total of 295 iPBS bands were observed among which 275 (93.22%) were found polymorphic. Mean Polymorphism information content (0.48) and diversity parameters including mean effective number of alleles (1.33), mean Shannon’s information index (0.33), overall gene diversity (0.19), Fstatistic (0.21), and inbreeding coefficient (1.00) reflected the presence of sufficient amount of genetic diversity in the studied plant materials. Analysis of molecular variance (AMOVA) showed that more than 40% of genetic variation was derived from populations. Model-based structure, principal coordinate analysis (PCoA) and unweighted pair-group method with arithmetic means (UPGMA) algorithms clustered the 131 safflower accessions into four main populations A, B, C, D and an unclassified population, with no meaningful geographical origin. Most diverse accessions originated from Asian countries including Afghanistan, Pakistan, China, Turkey, and India. Four accessions, Turkey3, Afghanistan4, Afghanistan2, and Pakistan24 were found most genetically distant and might be recommended as a candidate parents for breeding purposes. The findings of this study are most probably supported by the seven similarity centers hypothesis of safflower. This is a first study to explore the genetic diversity and population structure in safflower accessions using the iPBS-retrotransposon markers. The information provided in this work will therefore be helpful for scientists interested in safflower breeding. [ABSTRACT FROM AUTHOR]

Summary: The complete or partial loss of shattering ability occurred independently during the domestication of several crops. Therefore, the study of this trait can provide an understanding of the link between phenotypic and molecular convergent evolution. The genetic dissection of 'pod shattering' in Phaseolus vulgaris is achieved here using a population of introgression lines and next‐generation sequencing techniques. The 'occurrence' of the indehiscent phenotype (indehiscent versus dehiscent) depends on a major locus on chromosome 5. Furthermore, at least two additional genes are associated with the 'level' of shattering (number of shattering pods per plant: low versus high) and the 'mode' of shattering (non‐twisting versus twisting pods), with all of these loci contributing to the phenotype by epistatic interactions. Comparative mapping indicates that the major gene identified on common bean chromosome 5 corresponds to one of the four quantitative trait loci for pod shattering in Vigna unguiculata. None of the loci identified comprised genes that are homologs of the known shattering genes in Glycine max. Therefore, although convergent domestication can be determined by mutations at orthologous loci, this was only partially true for P. vulgaris and V. unguiculata, which are two phylogenetically closely related crop species, and this was not the case for the more distant P. vulgaris and G. max. Conversely, comparative mapping suggests that the convergent evolution of the indehiscent phenotype arose through mutations in different genes from the same underlying gene networks that are involved in secondary cell‐wall biosynthesis and lignin deposition patterning at the pod level. Significance Statement: Genetic mapping of the genetic architecture of pod shattering in common bean, and comparisons with other crops, have allowed the genetic basis of phenotypic convergent evolution to be defined. This definition indicates that different genes can be responsible for the shattering phenotype in legumes. [ABSTRACT FROM AUTHOR]

Smut disease caused by the fungal pathogen Thecaphora frezii Carranza & Lindquist is threatening the peanut production in Argentina. Fungicides commonly used in the peanut crop have shown little or no effect controlling the disease, making it a priority to obtain peanut varieties resistant to smut. In this study, recombinant inbred lines (RILs) were developed from three crosses between three susceptible peanut elite cultivars (Arachis hypogaea L. subsp. hypogaea) and two resistant landraces (Arachis hypogaea L. subsp. fastigiata Waldron). Parents and RILs were evaluated under high inoculum pressure (12000 teliospores g-1 of soil) over three years. Disease resistance parameters showed a broad range of variation with incidence mean values ranging from 1.0 to 35.0% and disease severity index ranging from 0.01 to 0.30. Average heritability (h2) estimates of 0.61 to 0.73 indicated that resistance in the RILs was heritable, with several lines (4 to 7 from each cross) showing a high degree of resistance and stability over three years. Evidence of genetic transfer between genetically distinguishable germplasm (introgression in a broad sense) was further supported by simple-sequence repeats (SSRs) and Insertion/Deletion (InDel) marker genotyping. This is the first report of smut genetic resistance identified in peanut landraces and its introgression into elite peanut cultivars. [ABSTRACT FROM AUTHOR]

Thickspike wheatgrass (Elymus lanceolatus [Scribn. & J.G. Sm.] Gould) is an important native perennial grass species used for rangeland revegetation in North America. Plant breeding efforts relying on space‐plant evaluations have resulted in limited improvement in this species. The purpose of this study was to characterize the performance of thickspike wheatgrass half‐sib families under space‐plant and sward plot evaluations, estimate the correlation between measured traits in both evaluation settings, and determine the validity of selecting thickspike wheatgrass for rangeland revegetation in the nontarget environment space‐plant plots. The study included 50 thickspike wheatgrass half‐sib families and five commercial cultivars and experimental populations which were evaluated over 3 years in space‐plant and sward plot evaluations at a field site in Box Elder County, Utah, USA. Collected data included stand percentage, flag leaf height, and herbage dry mass. Narrow‐sense heritability estimates were low to moderate (h2 < 0.60) and Spearman and genetic correlation estimates among traits were also generally low to moderate. Overall, there was little evidence to suggest the use space‐plant evaluations in thickspike wheatgrass improvement programmes. [ABSTRACT FROM AUTHOR]

Amino acid transporters (AATs) play an important role in transport process of various amino acids, which are indispensable in plant growth and development, while many putative AATs have been identified and the complete genomic sequences of the important plants have already been completed by splicing and assembling. There is still little knowledge about the expression, regulation and various biological functions of AATs in plants, including the major food crops. This study mainly reviewed the expression, regulation and various biological functions of AATs in plants, and the application of AATs in crop genetic improvement was also prospected. Thus, this review will provide important information for genetic improvement of staple food crops in plants. [ABSTRACT FROM AUTHOR]

Whole-chromosome painting probes were developed for each of the 10 chromosomes of maize by producing amplifiable libraries of unique sequences of oligonucleotides that can generate labeled probes through transcription reactions. These paints allow identification of individual homologous chromosomes for many applications as demonstrated in somatic root tip metaphase cells, in the pachytene stage of meiosis, and in interphase nuclei. Several chromosomal aberrations were examined as proof of concept for study of various rearrangements using probes that cover the entire chromosome and that label diverse varieties. The relationship of the supernumerary B chromosome and the normal chromosomes was examined with the finding that there is no detectable homology between any of the normal A chromosomes and the B chromosome. Combined with other chromosomelabeling techniques, a complete set of whole-chromosome oligonucleotide paints lays the foundation for future studies of the structure, organization, and evolution of genomes. [ABSTRACT FROM AUTHOR]

Crop productivity is highly dependent on the application of N fertilizers, but ever-increasing N application is causing serious environmental impacts. To facilitate the development of new wheat cultivars that can thrive in low N growth conditions, key loci and genes associated with wheat responses to low N must be identified. In this GWAS and t-test study of 190 M6 mutant wheat lines (Jing 411-derived) based on genotype data from the wheat 660k SNP array, we identified a total of 221 significant SNPs associated four seedling phenotypic traits that have been implicated in resistance to low N: relative root length, relative shoot length, relative root weight, and relative shoot weight. Notably, we detected large numbers of significantly associated SNP in what appear to be genomic ‘hotspots’ for resistance to low N on chromosomes 2A and 6B, strongly suggesting that these regions are functionally related to the resistance phenotypes that we observed in some of the mutant lines. Moreover, the candidate genes, including genes encoding high-affinity nitrate transporter 2.1, gibberellin responsive protein, were identified for resistance to low N. This study raises plausible mechanistic hypotheses that can be evaluated in future applied or basic efforts by breeders or plant biologists seeking to develop new high-NUE wheat cultivars. [ABSTRACT FROM AUTHOR]

Highlights • High levels of variations in bioactive compounds were observed among Glechoma longituba populations. • High genetic variations between populations of Glechoma longituba , but low genetic diversities within populations. • Good adaptabilities of Glechoma longituba to high variation of climatic and edaphic conditions. • Soil chemical property and climate act as the key points affecting the bioactive compounds of Glechoma longituba. Abstract Glechoma longituba is a widespread crop in China. With high concentrations of many bioactive compounds, it has long been treated as a health beneficial ingredient for human diet and even some medicine. In order to gain comprehensive understandings of current resources of Glechoma longituba , samples from seventeen geographical origins in fifteen Chinese provinces were collected to reveal the connections between different influence factors and certain bioactive compounds. Firstly, high variations in the contents of ethanol-soluble extracts, total flavonoid, chlorogenic acid, caffeic acid, rosmarinic acid, oleanolic acid and ursolic acid were proved among different Glechoma longituba populations. Totally four parameters of soil physical properties, twelve parameters of soil chemical properties, thirty years' climate records and genetic diversity among different Glechoma longituba populations were thoroughly investigated. As a result, soil chemical property and climate condition with significant correlation between each other were both indicated to have the strongest positive correlations with bioactive compounds of Glechoma longituba , among which soil phosphorus, soil iron, temperature and moisture were showed to act as key factors. Neither the genetic variation nor the soil physical property was significantly related to the concentrations of bioactive compounds. These results laid the first theoretical foundation for further study of how to improve the quality of Glechoma longituba resources, as well as provided guidance for breeders to focus more on choosing planting areas with ideal climate conditions and modulating the optimum soil chemical properties for better Glechoma longituba cultivation. [ABSTRACT FROM AUTHOR]

Understanding of genetic diversity is important to explore existing gene in any crop breeding program. Most of the diversity preserved in the landraces which are well–known reservoirs of important traits for biotic and abiotic stresses. In the present study, the genetic diversity at twenty-four most significant blast resistance gene loci using twenty-eight gene specific markers were investigated in landraces originated from nine diverse rice ecologies of India. Based on phenotypic evaluation, landraces were classified into three distinct groups: highly resistant (21), moderately resistant (70) and susceptible (70). The landraces harbour a range of five to nineteen genes representing blast resistance allele with the frequency varied from 4.96% to 100%. The cluster analysis grouped entire 161 landraces into two major groups. Population structure along with other parameters was also analyzed to understand the evolution of blast resistance gene in rice. The population structure analysis and principal coordinate analysis classified the landraces into two sub–populations. Analysis of molecular variance showed maximum (93%) diversity within the population and least (7%) between populations. Five markers viz; K3957, Pikh, Pi2–i, RM212and RM302 were strongly associated with blast disease with the phenotypic variance of 1.4% to 7.6%. These resistant landraces will serve as a valuable genetic resource for future genomic studies, host–pathogen interaction, identification of novel R genes and rice improvement strategies. [ABSTRACT FROM AUTHOR]

The European Food Safety Authority (EFSA) mandates two sets of statistical tests in the comparative assessment of a genetically-modified (GM) crop: difference testing to demonstrate whether the GM crop is different from its appropriate non-traited control; and equivalence testing to demonstrate whether it is equivalent to conventional references with an history-of-safe-use. The equivalence testing method prescribed by EFSA confounds the so-called GM trait effect with genotypic differences between the reference varieties and non-traited control. Critically, these genotypic differences, which we define as a ‘control background effect’, are the result of conventional plant breeding. Thus, the result of EFSA equivalence testing often has little or nothing to do with the GM trait effect, which should be the sole focus of the comparative assessment. Here, an integrated method is introduced for both difference and equivalence testing that considers the differences of the three genotype groups (GM, control, and references) as a two-dimensional random variable. A novel statistical model is proposed, called the trait model, that treats the effects of the GM and control materials as fixed for their difference, and as random for their common background. For significance testing, the covariance structure of the three genotype groups is utilized to decompose the differences into the trait effect and the control background effect. The trait difference is then derived as a conditional mean, given the background effect. The comparative assessment can then focus on the conditional mean difference, which is independent of the control background effect. Furthermore, the trait model is flexible enough to include various types of genotype-by-environment (G×E) interactions inherent to the experimental design of the trial. Numerical evaluations and simulations show that this new method is substantially more efficient than the current EFSA method in reducing both Type I and Type II errors (protecting both the consumer and producer risk) after the background effect is removed from the test statistic, and successfully addresses two major criticisms (i.e. statistical model lack of G×E, and study-specific equivalence criterion) that have been raised. [ABSTRACT FROM AUTHOR]

Soybean aphid (Aphis glycines) is an invasive species in North America. For more than a decade, scientists have been working on host plant resistance, but the frequent identification of aphid isolates resistant (virulent) to soybean [Glycine max (L.) Merr.] traits has caused concern amongst stakeholders interested in aphid control. To explore the diversity and distribution of these virulent aphids, we sampled soybean fields throughout the north-central United States and southern Canada from 2011 through 2013. We evaluated soybean aphid performance on soybean cultivars containing Rag1, Rag2, and Rag3 loci and categorized them per standard biotypes. The soybean aphid biotypes were widely distributed across the sampled region. We also used the performance test scores to study the outliers and unexpected results according to biotype. Intrabiotypic variability is common in North America. [ABSTRACT FROM AUTHOR]