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Wheat ( Triticum spp and, particularly, T. aestivum L.) is an essential cereal with increased human and animal nutritional demand. Therefore, there is a need to enhance wheat yield and genetic gain using modern breeding technologies alongside proven methods to achieve the necessary increases in productivity. These modern technologies will allow breeders to develop improved wheat cultivars more quickly and efficiently. This review aims to highlight the emerging technological trends used worldwide in wheat breeding, with a focus on enhancing wheat yield. The key technologies for introducing variation (hybridization among the species, synthetic wheat, and hybridization; genetically modified wheat; transgenic and gene-edited), inbreeding (double haploid (DH) and speed breeding (SB)), selection and evaluation (marker-assisted selection (MAS), genomic selection (GS), and machine learning (ML)) and hybrid wheat are discussed to highlight the current opportunities in wheat breeding and for the development of future wheat cultivars., Competing Interests: The authors declare no conflict of interest., (© 2024 The Author(s). Published by IMR Press.)

Powdery mildew, caused by Blumeria graminis f. sp. tritici (Bgt), is a serious fungal disease that critically threatens the yield and quality of wheat. Utilization of host resistance is the most effective and economical method to control this disease. In our study, a wheat breeding line ShiCG15-009, released from Hebei Province, was highly resistant to powdery mildew at all stages. To dissect its genetic basis, ShiCG15-009 was crossed with the susceptible cultivar Yannong 21 to produce F 1 , F 2 and F 2:3 progenies. After genetic analysis, a single dominant gene, tentatively designated PmCG15-009, was proved to confer resistance to Bgt isolate E09. Further molecular markers analysis showed that PmCG15-009 was located on chromosome 2BL and flanked by markers XCINAU130 and XCINAU143 with the genetic distances 0.2 and 0.4 cM, respectively, corresponding to a physic interval of 705.14-723.48 Mb referred to the Chinese Spring reference genome sequence v2.1. PmCG15-009 was most likely a new gene differed from the documented Pm genes on chromosome 2BL since its different origin, genetic diversity, and physical position. To analyze and identify the candidate genes, six genes associated with disease resistance in the candidate interval were confirmed to be associated with PmCG15-009 via qRT-PCR analysis using the parents ShiCG15-009 and Yannong 21 and time-course analysis post-inoculation with Bgt isolate E09. To accelerate the transfer of PmCG15-009 using marker-assisted selection (MAS), 18 closely or co-segregated markers were evaluated and confirmed to be suitable for tracing PmCG15-009, when it was transferred into different wheat cultivars., (© 2023. The Author(s).)

Wheat (Triticum aestivum L.) contributes substantially to global food and nutritional security. With the growing demands under the constraints of depleting natural resources, environmental fluctuation, and increased risk of epidemic outbreaks, the task of increasing wheat production has become daunting. The factors responsible for first green revolution seem to be exhausting rapidly, and there is an immediate need to develop the technologies which can not only increase the wheat production but also sustain the same at a higher level without adversely affecting the natural resources. Understanding abiotic stress factors such as temperature, drought tolerance, and biotic stress tolerance traits such as insect pest and pathogen resistance in combination with high yield in plants is of paramount importance to counter climate change related adverse effects on the productivity of wheat crops. Thus, an important goal of wheat breeding is to develop high-yielding varieties with better nutritional quality and resistance to major diseases. Therefore, in this chapter, we present a judicious mixture of basic as well as applied research outlooks. We trust that the information covered in this chapter would bridge the much-researched area of stress in plants with the information to breed climate-ready crop cultivars to ensure food security in the future.

Selected reaction monitoring (SRM) is a targeted mass spectrometry technique that enables precise quantitation of hundreds of peptides in a single run. This technique provides new opportunities for multiplexed protein biomarker measurements. For precision plant breeding, DNA-based markers have been used extensively, but the potential of protein biomarkers has not been exploited. In this work, we developed an SRM marker panel with assays for 104 potato (Solanum tuberosum) peptides selected using univariate and multivariate statistics. Thereafter, using random forest classification, the prediction markers were identified for Phytopthora infestans resistance in leaves, P. infestans resistance in tubers, and plant yield in potato leaf secretome samples. The results suggest that the marker panel has the predictive potential for three traits, two of which have no commercial DNA markers so far. Furthermore, the marker panel was also tested and found to be applicable to potato clones not used during the marker development. The proposed workflow is thus a proof-of-concept for targeted proteomics as an efficient readout in accelerated breeding for complex and agronomically important traits.

With the development of new technologies in recent years, researchers have made significant progress in crop breeding. Modern breeding differs from traditional breeding because of great changes in technical means and breeding concepts. Whereas traditional breeding initially focused on high yields, modern breeding focuses on breeding orientations based on different crops' audiences or by-products. The process of modern breeding starts from the creation of material populations, which can be constructed by natural mutagenesis, chemical mutagenesis, physical mutagenesis transfer DNA (T-DNA), Tos17 (endogenous retrotransposon), etc. Then, gene function can be mined through QTL mapping, Bulked-segregant analysis (BSA), Genome-wide association studies (GWASs), RNA interference (RNAi), and gene editing. Then, at the transcriptional, post-transcriptional, and translational levels, the functions of genes are described in terms of post-translational aspects. This article mainly discusses the application of the above modern scientific and technological methods of breeding and the advantages and limitations of crop breeding and diversity. In particular, the development of gene editing technology has contributed to modern breeding research. [ABSTRACT FROM AUTHOR]

Marker-assisted selection (MAS) plays a crucial role in crop breeding improving the speed and precision of conventional breeding programmes by quickly and reliably identifying and selecting plants with desired traits. However, the efficacy of MAS depends on several prerequisites, with precise phenotyping being a key aspect of any plant breeding programme. Recent advancements in highthroughput remote phenotyping, facilitated by unmanned aerial vehicles coupled to machine learning, offer a non-destructive and efficient alternative to traditional, time-consuming, and labour-intensive methods. Furthermore, MAS relies on knowledge of marker-trait associations, commonly obtained through genome-wide association studies (GWAS), to understand complex traits such as drought tolerance, including yield components and phenology. However, GWAS has limitations that artificial intelligence (AI) has been shown to partially overcome. Additionally, AI and its explainable variants, which ensure transparency and interpretability, are increasingly being used as recognised problem-solving tools throughout the breeding process. Given these rapid technological advancements, this review provides an overview of state-of-theart methods and processes underlying each MAS, from phenotyping, genotyping and association analyses to the integration of explainable AI along the entire workflow. In this context, we specifically address the challenges and importance of breeding winter wheat for greater drought tolerance with stable yields, as regional droughts during critical developmental stages pose a threat to winter wheat production. Finally, we explore the transition from scientific progress to practical implementation and discuss ways to bridge the gap between cuttingedge developments and breeders, expediting MAS-based winter wheat breeding for drought tolerance. [ABSTRACT FROM AUTHOR]

Molecular markers are effective tools used to 'flag' the location of a specific gene or the inheritance of a definite trait. Markers are unique DNA fragments that can be identified inside the entire genome. The development of molecular markers combined with high throughput technologies have paved the way for achieving the desirable traits as well as induced biotic and abiotic stress tolerance in plant, which enhanced the crop breeding. Highly polymorphic molecular markers are developed for gene mapping, estimation of genetic diversity, finding out the evolution and phylogeny of crop, analysis of heterosis, assessment of diploid/haploid crops and genotyping of cultivars along with Marker Assisted Breeding (MAB)/Marker Assisted Selection (MAS). These are the most significant objectives for crop breeding. This review reveals about the role of various recently developed molecular markers in the improvement of crop. Molecular markers act as a "milestone" for the researchers who aim to enhance crop breeding. [ABSTRACT FROM AUTHOR]

Marker-assisted selection (MAS) plays a crucial role in crop breeding improving the speed and precision of conventional breeding programmes by quickly and reliably identifying and selecting plants with desired traits. However, the efficacy of MAS depends on several prerequisites, with precise phenotyping being a key aspect of any plant breeding programme. Recent advancements in high-throughput remote phenotyping, facilitated by unmanned aerial vehicles coupled to machine learning, offer a non-destructive and efficient alternative to traditional, time-consuming, and labour-intensive methods. Furthermore, MAS relies on knowledge of marker-trait associations, commonly obtained through genome-wide association studies (GWAS), to understand complex traits such as drought tolerance, including yield components and phenology. However, GWAS has limitations that artificial intelligence (AI) has been shown to partially overcome. Additionally, AI and its explainable variants, which ensure transparency and interpretability, are increasingly being used as recognised problem-solving tools throughout the breeding process. Given these rapid technological advancements, this review provides an overview of state-of-the-art methods and processes underlying each MAS, from phenotyping, genotyping and association analyses to the integration of explainable AI along the entire workflow. In this context, we specifically address the challenges and importance of breeding winter wheat for greater drought tolerance with stable yields, as regional droughts during critical developmental stages pose a threat to winter wheat production. Finally, we explore the transition from scientific progress to practical implementation and discuss ways to bridge the gap between cutting-edge developments and breeders, expediting MAS-based winter wheat breeding for drought tolerance.

A multi-parental population is an innovative tool for mapping large numbers of loci and genetic modifications, particularly where they have been used for breeding and pre-breeding in crops. Frost injury is an environmental stress factor that greatly affects the growth, development, production efficiency, and geographical distribution of crops. No reported study has focused on genetic mapping and molecular marker development using diallel populations of potatoes. In this study, 23 successful cross combinations, obtained by a half diallel cross among 16 parents, including eight frost-tolerant advanced breeding lines and eight cultivars, were used to map the genetic loci for frost tolerance and to create a molecular marker-assisted selection (MAS) system. Three candidate regions related to frost tolerance on chromosomes II, V, and IX were mapped by bulked segregant analysis (BSA). Furthermore, six SNP markers associated with frost tolerance from candidate regions were developed and validated. Above all, a MAS system for the frost tolerance screening of early breeding offspring was established. This study highlights the practical advantages of applying diallel populations to broaden and improve frost-tolerant germplasm resources. [ABSTRACT FROM AUTHOR]

• Berry skin color is one of the most important and extensively studied quality traits in grapevines. • Various molecular markers linked to berry color traits and genotyping strategies have been proposed, but none have proved robustness and effectiveness on different genetic backgrounds. • Deciphering the whole genome sequencing data revealed three high polymorphic regions linked to the berry color trait. • A High-Resolution Melting genotyping strategy involving three selected molecular markers proved an effective molecular-assisted selection strategy across diverse grapevine genetic backgrounds. Marker-assisted selection (MAS) represents one of the most effective strategies to reduce costs and time in plant breeding programs. MAS benefits from the identification of markers in strong linkage disequilibrium (LD) with causative genes and from the development of fast, scalable, and reproducible screening techniques. In grape, berry color is a valuable trait, highly related to the sensory characteristics of fresh grape and wine quality. The present work aims to develop a MAS strategy to select skin color by High-Resolution Melting (HRM), a 'close-tube' method capable of detecting polymorphisms within PCR-amplified DNA fragments. To identify molecular markers associated with the berry skin color phenotypic trait, the total genome of 3 white-berry and 3 red-berry accessions were sequenced using Illumina technology and aligned to the reference genome PN40024 v4. The sequencing results revealed the presence of three highly polymorphic regions on chromosome 2 between 15 Kbp and 17 Kbp for red berry genotypes. HRM analyses were carried out on a total of 95 genotypes, 70 of which comprised a berry color segregating population: ['Italia' (white berry) x cv 'Crimson Seedless' (red berry)] and 25 genotypes belonging to a commercial grapevine germplasm collection consisting of 11 red and 14 white berry accessions. The HRM profiles of the three regions tested strongly correlated with the phenotypic trait of color. The results of this work represent an effective, fast, and reliable genotyping strategy that enables the discrimination of genotypes based on the presence or absence of berry pigmentation. [ABSTRACT FROM AUTHOR]

Plant breeding for the generation of cultivars adapted to local conditions has been an important and strategic concern of developing countries with agriculture-based economies. Considering economic constraints, breeders must improve genetic gain to increase the delivery of better cultivars with lower costs, through the implementation of molecular breeding and rapid generation advance. The aim of this work is to assess the actual economic impact of the implementation of these technologies on genetic gain for yield, rice blast disease resistance, and grain amylose content in a conventional rice breeding program. This analysis is intended as a case study of public breeding programs in developing countries. To accomplish this objective, cost analyses and genetic gain estimations were performed for four rice breeding scenarios: conventional and marker-assisted selection, with and without rapid generation advance. These estimations were then used to develop a cost index reflecting the breeding efficiency. The most efficient method was found to depend on the objective trait considered. For yield, there are small variations in genetic gain, but in terms of costs, the application of technology increases the breeding efficiency. For rice blast resistance, marker-assisted selection is not an efficient option when not using rapid generation advance. Conversely, the efficiency of marker-assisted selection increases when using rapid generation advance. For grain amylose content, the greatest effect on genetic gain is obtained when using marker-assisted selection. Rapid generation advance always increases the breeding efficiency. The use of new technological tools is recommended in terms of the cost–benefit function. [ABSTRACT FROM AUTHOR]

The present paper summarized some knowledge of modern technologies, applied in apple (Malus domestica) genome studies. New generation sequencing allowed single nucleotide polymorphism (SNP) chip technologies for genotyping, description of functional apple genes, characterization of the evolutionary results in apple genome fragment transition, as well as phylogenetic reconstruction of the genus Malus, being the confirmed progeny of M. sieviersii. Based on these technologies, newly developed putative markers may give the most important biological data such as age, geographical origins, tissue type determination, and external visible characters. The new generation genotyping platforms, representing very high efficiency, are now successfully applied for random apple genome-wide association (GWA) studies as well pedigree-based analysis and marker-assisted selection (MAS). [ABSTRACT FROM AUTHOR]

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With the development of molecular marker technology in the 1980s, the fate of plant breeding has changed. Different types of molecular markers have been developed and advancement in sequencing technologies has geared crop improvement. To explore the knowledge about molecular markers, several reviews have been published in the last three decades; however, all these reviews were meant for researchers with advanced knowledge of molecular genetics. This review is intended to be a synopsis of recent developments in molecular markers and their applications in plant breeding and is devoted to early researchers with a little or no knowledge of molecular markers. The progress made in molecular plant breeding, genetics, genomic selection and genome editing has contributed to a more comprehensive understanding of molecular markers and provided deeper insights into the diversity available for crops and greatly complemented breeding stratagems. Genotyping-by-sequencing and association mapping based on next-generation sequencing technologies have facilitated the identification of novel genetic markers for complex and unstructured populations. Altogether, the history, the types of markers, their application in plant sciences and breeding, and some recent advancements in genomic selection and genome editing are discussed. [ABSTRACT FROM AUTHOR]

Cultivating resistant varieties of potato is the most effective and environmentally safe method of protecting against pests and diseases that affect potato crops. Therefore, potato breeding is focused on developing more resistant varieties so that the use of plant health products can be reduced during the cultivation cycle. Resistance to late blight, viruses and nematodes is the most important agricultural requirement. The use of molecular markers allows for the effective selection of resistant genotypes at early stages of breeding. However, the impact of early selection for resistance on the agronomic value of the final selected clones is a cause of concern for breeders. This study investigates the relationship between the presence of the combined resistance genes HI, Ry-fsto and Rpi-phul, which confer resistance to nematodes, potato virus Y and late blight, respectively, and certain agricultural traits. The agronomic performance of most clones with and without the identified resistance genes was similar in terms of tuber yield, tuber size, tuber shape regularity, eye depth and tuber defect intensity. Some combinations with Ry-fsto may produce higher yields but may also be associated with more tuber defects. No negative relationships were observed between the combined resistance genes HI + Ry-fsto + Rpi-phul and potato quality. [ABSTRACT FROM AUTHOR]

Sharka, caused by plum pox virus, is the most important viral disease of stone fruits. Important progresses have been recently achieved in apricot ( Prunus armeniaca), identifying a major locus on chromosome 1 which explains most of the variability for plum pox virus (PPV) resistance trait. A set of molecular markers associated with the resistance has been developed and validated in different genetic backgrounds, endorsing their application for breeding purposes. Particularly for complex traits as the PPV resistance, requiring long and expensive phenotyping procedures, marker-assisted selection (MAS) bears a great potential to improve the efficiency of conventional breeding. In this work, novel HRM (high-resolution melting) assays were designed for the genotyping of resistant/susceptible alleles at PPV resistance (PPVres) locus. The assays were tested on 51 apricot cultivars and breeding selections already phenotyped for PPV resistance and cross-validated with standard short simple repeat marker data. We demonstrated that three HRM assays, PGS1.21_SNP, PGS1.24_SNP, and ZP002_DEL, represent a reliable, quick, and cost-effective genotyping approach, particularly suitable as high-throughput screening method for large-scale breeding programs. [ABSTRACT FROM AUTHOR]

Plant growth as well as productivity of rice (Oryza sativa L.), the major cereal and staple food of millions, is significantly affected by numerous biotic and abiotic stresses. Among these, drought stress is one of the major constraints for production and yield stability of rice in rainfed ecosystem. Hence rice varieties/genotypes with drought tolerance must be identified urgently. The main objectives of the present study were screening of seedlings of various rice genotypes for drought tolerance by conventional method and molecular characterisation of selected rice genotypes for drought tolerance using microsatellite markers. Twenty one rice genotypes obtained from the Plant Breeding Division, RARS, Pattambi, were used for the study. Initially, seedlings of these genotypes were subjected to conventional drought screening with PEG-6000 (6 MPa and 8 MPa). Out of the 21 rice genotypes, only fourteen genotypes were selected based on seedling vigour index and used for molecular characterisation. DNA extraction of samples was performed by CTAB method followed by PCR amplification with two specific SSR markers, viz., RM103 and RM212. Monomorphic bands were observed with RM103 for all the fourteen genotypes; hence it cannot be considered as a suitable marker for drought tolerance in these genotypes. Polymorphic bands were observed in the studied genotypes for the marker RM212. However, linkage between RM212 marker with the seedling vigour index under drought stress was not significant. Hence, further research with other linked SSR markers must be carried out for marker assisted selection for drought tolerance in these rice genotypes. [ABSTRACT FROM AUTHOR]

Although thousands of scientific articles have been published on the subject of marker-assisted selection (MAS) andquantitative trait loci (QTL), the application of MAS for QTL in plant breeding has been restricted. Among the main causes for thislimited use are the low accuracy of QTL mapping and the high costs of genotyping thousands of plants with tens or hundreds ofmolecular markers in routine breeding programs. Recently, new large-scale genotyping technologies have resulted in a costreduction. Nevertheless, the MAS for QTL has so far been limited to selection programs using several generations per year, wherephenotypic selection cannot be performed in all generations, mainly in recurrent selection programs. Methods of MAS for QTL inbreeding programs using self-pollination have been developed.

The cytoplasmic male sterile line system comprising CRMS 32A and its maintainer line CRMS 32B is a popular choice for the development of new hybrids in India as CRMS 32A, having Kalinga 1 cytoplasm (other than WA), is a viable alternative to WA cytoplasm. However, both lines are susceptible to bacterial blight (BB), a major disease on rice. As enhancement of host plant resistance is the most effective and economical strategy to control this disease, four resistance genes (Xa4, xa5, xa13, and Xa21) were transferred from a BB pyramid line of IR64, into the A and B lines using a marker-assisted backcrossing (MAB) breeding strategy. During the transfer of genes into CRMS 32B, foreground selection was applied using markers associated with the genes, and plants having resistance alleles of the donor, are selected. Selection for morphological and quality traits was practiced to select plants similar to the recurrent parent. The four gene and three gene pyramid lines exhibited high levels of resistance against the BB pathogen when challenged with eight virulent isolates. Using genome wide based SSR markers for background selection, pyramids having >95% of the recurrent parent genome were identified. With CRMS 32B gene pyramid as donor, the four resistance genes were transferred into the A line through repeated backcrosses and the A line pyramids also exhibited high level of resistance against BB. Through a combination of selection at phenotypic and molecular levels, four BB resistance genes were successfully introduced into two parental lines (CRMS 32 B and A) of Rajalaxmi, an elite popular hybrid. The pyramided B lines did exhibit high levels of resistance against BB. Selection for morphological and quality traits and background selection hastened the recovery of the recurrent parent genome in the recombinants. Through repeated backcrosses, all the four resistance genes were transferred to CRMS 32A and test crosses suggest that the maintenance ability of the improved CRMS 32B lines is intact. These improved maintainer and CMS lines can directly be used in hybrid rice breeding and the new hybrids can play an important role in sustainable rice production in India. [ABSTRACT FROM AUTHOR]

Oriental persimmon (Diospyros kaki) originated in Eastern Asia, and many indigenous cultivars have been developed in China, Japan, and Korea. These cultivars are classified intofour groups based on their natural astringency loss on the tree and seed formation: pollination-constant non-astringent (PCNA), pollinationvariant non-astringent (PVNA), pollination-constant astringent (PCA), and pollination-variant astringent (PVA). PCNA is the most desirable type because the fruit can be eaten without any postharvest treatment; therefore, one of the goals of our persimmon breeding programs is to release superior PCNA cultivars. The PCNA genotype is recessive to the other three non-PCNA genotypes, and PCNA-type F1 offspring are obtained exclusively from crosses among PCNA genotypes. Moreover, the number of superior PCNA crossparents have been limited. In the late 1980s, inbreeding depression became obvious, especially in terms of fruit size, tree vigor, and productivity. To mitigate the inbreeding, a backcross program using PCNA [(non- PCNA × PCNA) × PCNA] was started in 1990. This process, however, was inefficient because only 15% of the offspring were PCNA, and all offspring had to be grown to the fruiting stage. Therefore, molecular markers linked to the PCNA locus were developed for discriminating PCNA offspring. A molecular marker linked to Chinese PCNA has also been developed. [ABSTRACT FROM AUTHOR]

Biotic stresses are a potential threat to global food security. The origin of new pathogens and insect races due to climatic and genetic factors is a major challenge for plant breeders in breeding biotic stress resistant crops. Yield losses due to biotic stresses have resulted in 800 million people underfed in the world. Reduced yield due to biotic stresses and increasing food demand put international food security at risk as 70% more food will be required in 2050. This review describes and compares the conventional and molecular genetics methods being used for breeding biotic stress resistant crops. In the past, classical breeding approaches like introduction, hybridization, composite crossing, multiline, and backcross breeding were utilized for this purpose. However, these methods were slow, expensive, and hectic for developing resistance in crops. Furthermore, breakdown of resistance due to fast evolving pathogens could not be coped with using these time consuming methods. Therefore, molecular genetics approaches like mutation, marker assisted selection (MAS), genomics, recombinant DNA technology, targeted induced local lesions in genome (TILLING), and virus induced gene silencing (VIGS) were adapted by breeders to develop effective resistance in crop plants in a shorter time. TILLING, being a nontransgenic method, is expected to become the most powerful tool for this purpose. [ABSTRACT FROM AUTHOR]

Downy mildew is a fungal disease of sunflower that can lead to severe yield losses. The damage caused by the pathogen can be controlled by growing resistant sunflower varieties. Gene Pl was introgressed into cultivated sunflower from the wild species Helianthus argophyllus and provides resistance against all known downy mildew races. In this study, we used a mapping population from the cross-RHA 419/RHA-N-49. We identified a new co-segregating simple sequence repeat marker ORS675 and confirmed the co-segregation of markers ORS716 and ORS662 with Pl gene. The markers were validated on two registered resistant inbred lines RHA 443 and RHA 464, as well as on twenty inbred lines RH 1-20 obtained through methods of classical breeding. Molecular marker ORS716 was assessed for usefulness in selecting resistant progeny in 12 BC populations. Markers were found to be valuable for molecular breeding in diverse genetic backgrounds and enabled transfer of the resistance gene in different sunflower genotypes. [ABSTRACT FROM AUTHOR]

Globe artichoke ( Cynara cardunculus var. scolymus), whose immature inflorescences ( capitula) are consumed as a vegetable all over the world, contributes significantly to the agricultural economy of the Mediterranean basin. Here, we describe a QTL (quantitative trait loci) analysis aimed at elucidating the mode of inheritance of seven main and first-order capitulum traits. Mapping was carried out in an F population obtained by crossing a globe artichoke with a cultivated cardoon ( C. cardunculus var. altilis). A total of 100 QTL associated with the seven capitulum traits were mapped to 23 chromosomal regions, scattered over 12 of the 17 linkage groups. Among these, 73 were expressed in both growing seasons, while the others were only detected in one season. Up to nine QTL per trait were identified, and major QTL, responsible for some 20 % of the phenotypic variation, were detected for capitulum length, diameter, shape index and fresh weight. The QTL for correlated traits frequently co-localized, most likely due to pleiotropy. This study represents the first report on yield traits QTL in globe artichoke. The QTL identified, along with linked markers, particularly those located in four hot-spot QTL regions are of practical interest for crop improvement based on marker-assisted breeding. [ABSTRACT FROM AUTHOR]

Over the past three decades, molecular marker studies reached extraordinary advances, especially for sequencing and bioinformatics techniques. Marker-assisted selection became part of the breeding program routines of important seed companies, in order to accelerate and optimize the cultivar developing processes. Private seed companies increasingly use marker-assisted selection, especially for the species of great importance to the seed market, e.g. corn, soybean, cotton, and sunflower. In the Brazilian public institutions few breeding programs use it efficiently. The possible reasons are: lack of know-how, lack of appropriate laboratories, few validated markers, high cost, and lack of urgency in obtaining cultivars. In this article we analyze the use and the constraints of marker-assisted selection in plant breeding programs of Brazilian public institutes. [ABSTRACT FROM AUTHOR]

Quantitative trait locus (QTL) analyses have greatly enhanced our understanding of complex traits in rice ( Oryza sativa). In parallel, the development of introgression lines has provided a powerful tool for elucidation of complicated genetic networks and identification of QTL. We recently developed a biotron breeding system that allows rapid indoor cultivation of rice plants. The system, however, has two relatively weak points in its application to marker-assisted breeding in rice: first, variation in generation times among cultivars; second, the low number of seeds produced by crosses. To compensate for these weaknesses, we propose utilizing cytoplasmic male sterility (CMS) and restorer (Rf) lines with a cv. Nipponbare genetic background. Through use of the Nipponbare genetic background, rice generation times of 2 months can be achieved regardless of any differences in the genetic background of the donor rice plant. This CMS–Rf system confers a high yield of hybrid seeds, avoids the need for emasculation and precludes accidental crosses. Our results demonstrate that this new methodology can markedly accelerate many different aspects of rice research, especially in functional genomics. The combination of biotron breeding system, early flowering habit and CMS will be of great value for screening candidate genes associated with QTL and for introducing useful QTL into elite cultivars. [ABSTRACT FROM AUTHOR]

The evaluation and use of the vast diversity contained in plant genetic resources (PGR) is a main challenge for today's plant breeding. The use of molecular markers has hugely increased the knowledge about genetic diversity and great hopes are raised about the potential of marker assisted selection [MAS; sometimes also termed SMART breeding (Selection with Markers and Advanced Reproductive Technologies)] to help increasing the use of PGR and maintaining crop genetic diversity. Another approach growing attention has been paid to over the past two decades and which also aims to increase variation in crops is evolutionary and participatory breeding (EPB). In this paper we discuss both the potential of marker-assisted breeding strategies and the potential of EPB breeding to contribute to the maintenance, increase and development of agrobiodiversity. The potentials of molecular markers in the evaluation and use of PGR and their documented contribution to agrobiodiversity are reviewed and results from guided interviews with scientists and breeders are given. Despite tremendous research efforts involving molecular markers, it is still difficult to obtain a clear picture how molecular markers contribute to the use of PGR in plant breeding. Minor and major crops do not benefit to the same degree from recent developments in marker technology. It therefore depends at least in part on economic considerations whether SMART breeding or EPB strategies or both are implemented in the breeding process of a crop. A general decision in favor or against MAS or EPB when breeding for diversity would not yield optimum results. [ABSTRACT FROM AUTHOR]

Geneticists and breeders are positioned to breed plants with root traits that improve productivity under drought. However, a better understanding of root functional traits and how traits are related to whole plant strategies to increase crop productivity under different drought conditions is needed. Root traits associated with maintaining plant productivity under drought include small fine root diameters, long specific root length (SRL), and considerable root length density, especially at depths in soil with available water. In environments with late season water deficits, small xylem diameters in targeted seminal roots save soil water deep in the soil profile for use during crop maturation and result in improved yields. Capacity for deep root growth and large xylem diameters in deep roots may also improve root acquisition of water when ample water at depth is available. Xylem pit anatomy that makes xylem less 'leaky' and prone to cavitation warrants further exploration holding promise that such traits may improve plant productivity in water-limited environments without negatively impacting yield under adequate water conditions. Rapid resumption of root growth following soil rewetting may improve plant productivity under episodic drought. Genetic control of many of these traits through breeding appears feasible. Several recent reviews have covered methods for screening root traits but an appreciation for the complexity of root systems (e.g. functional differences between fine and coarse roots) needs to be paired with these methods to successfully identify relevant traits for crop improvement. Screening of root traits at early stages in plant development can proxy traits at mature stages but verification is needed on a case by case basis that traits are linked to increased crop productivity under drought. Examples in lesquerella (Physaria) and rice (Oryza) show approaches to phenotyping of root traits and current understanding of root trait genetics for breeding. [ABSTRACT FROM AUTHOR]

The primary aim of plant breeders is to develop new cultivars in order to improve productivity and to combat threats from pests and diseases. Recent advances in genomics have been recognised as providing important tools for plant breeders in the form of molecular genetic markers that can be used to tag genes of interest. However, the cost-effective use of marker technology is dependent on the nature and timing of the use of such markers. A conventional potato breeding programme typically creates a large breeding population and then employs phenotypic recurrent selection over a number of generations to identify superior genotypes. Marker-assisted selection (MAS) provides the advantage of being applicable at the seedling or an early generation stage. We have analysed the cost of MAS and compared it to conventional screening, then modelled the respective costs against the breeding population size of the generation in which they would be applied to determine whether MAS in the early generations of a potato breeding programme would be cost-effective. As various potato breeding programmes employ different selection rates in early generations, these rates have also been modelled to determine the effect. Our results indicate that MAS could be applied cost-effectively in the second clonal generation for all models currently employed in potato breeding. [ABSTRACT FROM AUTHOR]

DNA markers have a large potential to improve efficiency and precision of conventional plant breeding programmes based on marker-assisted selection ( MAS). In our study, we have evaluated the predictive abilities of the SCAR marker RYSC3 and the CAPS marker GP122564 with regard to the PVY resistance genes Ry adg and Ry sto, respectively, and of marker TG689 linked to H1 conferring resistance to Globodera rostochiensis and marker HC associated with high levels of G. pallida resistance. The evaluations were made in 28 cultivars and accessions and in 219 progeny genotypes descending from ten different crosses. We observed in all evaluated cultivars and accessions the expected marker patterns according to their phenotypic classification into resistant and susceptible genotypes. However, in part considerable discrepancies were observed when analysing progeny of controlled crosses involving these resistance sources, particularly with respect to H1. Based on these results, practical aspects for the efficient implementation of marker-assisted selection are discussed, which consider the genetic origin of the material, costs aspects and methodology applied. [ABSTRACT FROM AUTHOR]

The brown planthopper (BPH) is the most devastating insect pest in rice-producing areas. Shanyou 63 has become a widely cultivated hybrid in China over the last two decades; however, this line has become increasingly susceptible to bacterial blight (BB), blast, and BPH, resulting in a rapid decline in its use in rice production. In this study, a molecular marker-assisted selection (MAS) introgression of Bph14 and Bph15 was performed to improve the BPH resistance of Minghui 63 and its derived hybrids such as Shanyou 63. The effect of pyramiding genes was then comprehensively evaluated using three tests that comprised seedbox screening, feeding rate, and antixenosis for settling in the field. The results showed that the improved hybrids containing a single BPH resistance gene showed enhanced resistance (lower resistance score, honeydew weight and number of BPH settling) compared to conventional hybrids, while pyramiding two genes provided even higher resistance. Moreover, both Bph14 and Bph15 are partial dominance genes, and have a strong dosage effect on the resistance to BPH in the hybrid background, which is useful for breeding BPH-resistant hybrids. Field trial data demonstrated that yields of improved hybrid rice were higher than or similar to the control (Shanyou 63) under natural field conditions. These improved versions could be used in breeding programs for 'green super rice.' [ABSTRACT FROM AUTHOR]

Abstract: This study was conducted to assess the genetic basis and develop a regression model for a QTL trait, fruit setting of a full sib population of 164 hybrids obtained between ‘Clementine’ mandarin (Citrus reticulata Blanco ‘Clementine) and ‘Orlando’ tangelo’ (Citrus paradisi Macf. ‘Duncan’× C. reticulata Blanco ‘Dancy’). Fruit setting of a 164 full sib population field-planted in 2007 was evaluated by visual counting of fruits in 2008, 2009, and 2010. We estimated linkage groups and effects of QTLs by using MapQTL5. Based on interval mapping, seven linkage groups of the maternal and eight linkage groups of the paternal maps harboured QTLs of the fruits setting, covering a total 300 of 1744cM Citrus map. Only three segments were associated with all three-year data (one in ‘Clementine’ and two in ‘Orlando’ map) spanning 60cM of 1744cM of Citrus linkage map. Twenty-seven (17%) and 13 (8%) hybrids consistently produced less than 5 fruits and the highest number of fruits (≥50) in their 2nd, 3rd, and 4th ages. Based on BACKWARD elimination procedure of PROC REG option nested in SAS program, regression models constructed for 2008, 2009, and 2010s fruit setting explained 35, 81, and 38% of the total phenotypic variation (R 2) observed in the 164 full-sib hybrids, respectively (P ≤0.05). This study indicated that early fruit setting was a complex trait affected by many QTLs and the regression model developed in this study might be used to predict performances of hybrids with similar genetic background. [Copyright &y& Elsevier]

Conventional plant breeding is primarily based on phenotypic selection of superior individuals among segregating progenies resulting from hybridization. It is often time consuming as breeding a new cultivar takes between eight and ten years and even then, the release of improved cultivar is not guaranteed. Hence, breeders are extremely interested in new technologies that could make this procedure more efficient. Marker-assisted selection, often simply referred to as Marker-Assisted Selection (MAS) offers such a possibility by adopting a wide range of novel approaches to improving the selection strategies in crop breeding. Molecular markers are powerful research tools that make it possible to determine the genetic makeup of plants; for that it is possible the selection by plants genotype. In this paper, we refer the significant advancements towards application of molecular marker technology for crop improvement in the last decade, in tomato. Finally, we discuss reasons why the greater adoption of MAS in the future is inevitable, although the extent of its use will depend on available resources, and may be delayed in less-developed countries. [ABSTRACT FROM AUTHOR]

Citrus kinokuni 'Mukaku kishu' PI539530 and its progeny were studied to identify random amplified polymorphie DNA (RAPD) primers associated with seedlessness. Ninety-one F1 [(Robinson op) x C. kinokuni] individuals showed a 1:1 segregation ratio between seedless and seeded phenotypes with seedless as a single dominant gene. Bulked segregant analysis was used to identify markers associated with the seedless locus. Eighteen RAPD primers were mapped into a partial linkage group (≈55.8 cM length) with four RAPD primers flanking the seedless locus: OPAIll-0.8 at 8.7 cM, OPAJI9-1.0 at 8.4 cM, OPM06r-0.85 at 4.3 cM, and OPAJ04r-0.6 at 6.4 cM. The identification of molecular markers linked to C. kinokuni Fs seedless locus constitutes an important and major tool for citrus breeding and selection. [ABSTRACT FROM AUTHOR]

In the past 20 years, the major effort in plant breeding has changed from quantitative to molecular genetics with emphasis on quantitative trait loci (QTL) identification and marker assisted selection (MAS). However, results have been modest. This has been due to several factors including absence of tight linkage QTL, non-availability of mapping populations, and substantial time needed to develop such populations. To overcome these limitations, and as an alternative to planned populations, molecular marker–trait associations have been identified by the combination between germplasm and the regression technique. In the present preview, the authors (1) survey the successful applications of germplasm–regression–combined (GRC) molecular marker–trait association identification in plants; (2) describe how to do the GRC analysis and its differences from mapping QTL based on a linkage map reconstructed from the planned populations; (3) consider the factors that affect the GRC association identification, including selections of optimal germplasm and molecular markers and testing of identification efficiency of markers associated with traits; and (4) finally discuss the future prospects of GRC marker–trait association analysis used in plant MAS/QTL breeding programs, especially in long-juvenile woody plants when no other genetic information such as linkage maps and QTL are available. [ABSTRACT FROM AUTHOR]

Molecular breeding for pathogen resistance faces two major problems that delay its widespread adoption, resistance breakdown and difficulties in unambiguously identifying the alleles of the markers associated with specific resistance genes. Since the breakdown of the Rvi6 ( Vf) gene in the Northern part of Europe breeders have intensified the search for new resistance sources to be introduced into their breeding programs. Alternative major genes to Rvi6 are available (e.g. Rvi2, Rvi4, Rvi5, Rvi10; Rvi11, Rvi12, Rvi13, and Rvi15, respectively Vh2, Vh4, Vm, Va, Vbj, Vb, Vd, Vr2 according to the old apple scab resistance gene nomenclature) but, with few exceptions (i.e., Rvi4, Rvi5 and, Rvi13), they have so far not been incorporated in commercial varieties. Pyramiding, i.e., combining several of these major resistance genes (R-genes) in individual plants, is one of the most promising strategies currently available to develop apple cultivars with durable apple scab resistance. But, which genes are the best suited to produce such new cultivars? Although the most interesting genes are surely those whose resistance so far has not been broken by the pathogen, genes with resistance that has been overcome coupled with only limited spread of the virulence may also be used in the pyramiding process. However, obtaining information on whether an R-gene is overcome and if so, the extent of the spread of the virulence is difficult and time consuming. Furthermore, often such reports are not up-to-date and the correctness of the data is difficult to verify. To solve these problems, the initiative “Monitoring of Venturia inaequalis virulences” has been proposed. The monitoring is based on a network of orchards of selected differential hosts. Incidence and severity of scab on these genotypes will be collected yearly; and after validation, the data will be published through the homepage of the project (). Here, we present an outline of this initiative. A second major obstacle for broad adoption of marker assisted selection is the lack of tools to align marker analyzes performed in different laboratories to unambiguously identify the alleles linked to specific resistances. The identification of the alleles of the markers in coupling with the resistance genes is often very difficult, if the same genotype used to develop the markers is not simultaneously analyzed. In this paper we present an approach to standardize the size of the alleles in coupling with the resistance genes, using easily accessible cultivars. The proposed procedure has been applied to selected markers for the apple scab resistance genes Rvi2, Rvi4, Rvi5, Rvi6, Rvi11, Rvi12, Rvi13, Rvi14 and Rvi15 (respectively Vh2, Vh4, Vm, Vf, Vbj, Vb, Vd, Rvi14 and Vr2 according to the old nomenclature). [ABSTRACT FROM AUTHOR]

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Abstract: ‘Khao Dawk Mali 105’ (KDML105), a Thai aromatic rice cultivar, has been accepted in markets as a prime jasmine rice with premium prices. It has been extensively used as a parental line to develop new cultivars for rainfed lowland areas in Thailand because of its favorable quality and fragrance. However, this cultivar is highly susceptible to brown planthopper (BPH), a phloem sap-feeding insect pest of rice. The main objective of this study was to combine KDML105 essential grain quality traits with BPH resistance from the donor cultivar, ‘Rathu Heenati’. The linkage drag between Bph3 and Wx a alleles was successfully broken by phenotypic and marker-assisted selections. All introgression lines (ILs) developed in this study showed a broad spectrum resistance against BPH populations in Thailand and had KDML105 grain quality standards. Finally this study was revealed that the ILs can be directly developed into BPH resistant varieties or can be used as genetic resources of BPH resistance to improve rice varieties with the Wx b allele in rice breeding programs. [Copyright &y& Elsevier]

We have previously identified 2 RAPD and 8 AFLP markers that were associated with yellow seed coat gene in a stable and pure yellow-seeded DH line No. 2127-17, however, they were not suitable in large-scale MAS. In this paper, it reported our efforts in developing rapid and reliable SCAR and CAPS markers from the RAPD and AFLP markers. Based on the sequence information in the regions of the most closely linked 4 AFLP and 2 RAPD markers, one SCAR (SCS1130) and one CAPS (SCA1) maker were successfully developed. Linkage analysis on a 127 DH lines population derived from the cross Hui5148-2 × No. 2127-17 revealed that they were tightly flanked (3.2 cM, 3.8 cM respectively). The resulting SCS1130 and SCA1 were further evaluated in backcross breeding families and demonstrated more accurate and valuable in MAS breeding. The development of these new markers would facilitate and accelerate the yellow seed coat breeding in Brassica napus. [ABSTRACT FROM AUTHOR]

There is an increasing amount of public sequence information for the main cultivated cereals, such as wheat and barley. It is not foreseeable that comparable efforts or resources could be devoted to related wild species. However, wild species are interesting sources of genetic variation through introgression breeding. Comparative genomics can be a helpful approach to make use of the available genomic resources. In this context, the potential of the wild barley species Hordeum chilense has been explored in recent years. It exhibits great levels of polymorphism and high crossability with different cereal genera. In addition, interesting biotic and abiotic stress resistance genes, and important quality traits like carotene content and seed storage protein variability shown in the species are also expressed in wheat backgrounds, and are the basis of a breeding program. Different approaches have been undertaken for tagging H. chilense genomic regions in a wheat background. The search for the most suitable DNA marker system started with the development of RAPD and SCAR markers due to a lack of sequence information from the wild species. Transferability of markers from wheat and barley (like STSs or SSRs) have also been useful approximations. More recently, SNP development is being accomplished for the species. In this work, the situation and prospects with the available molecular tools are considered from a practical point of view. [ABSTRACT FROM AUTHOR]

• CRISPR/Cas9 ultimately works on site specific nucleases such as ZFNs or TALENs. • Revolutionized CRISPR technology assists researchers for enhanced genome editing. • The era has changed from the conventional use of molecular marker to CRISPR/Cas9 system. • The HDR tool functions to knock-in DNA fragment, as well as allele replacements and recoded genes. • CRISPR/Cas9 system promises a more proven genomic relocation in the coming future. The advent of genetic selection and genome modification method assure about a real novel reformation in biotechnology and genetic engineering. With the extensive capabilities of molecular markers of them being stable, cost-effective and easy to use, they ultimately become a potent tool for variety of applications such a gene targeting, selection, editing, functional genomics; mainly for the improvisation of commercially important crops. Three main benefits of molecular marker in the field of agriculture and crop improvement programmes first, reduction of the duration of breeding programmes, second, they allow creation of new genetic variation and genetic diversity of plants and third most promising benefit is help in production of engineered plant for disease resistance, or resistance from pathogen and herbicides. This review is anticipated to present an outline how the techniques have been evolved from the simple conventional applications of DNA based molecular markers to highly throughput CRISPR technology and geared the crop yield. Techniques like using Zinc Finger Nucleases (ZFNs), Transcription Activator-Like Effector Nucleases (TALENs) and Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR/Cas9) systems have revolutionised in the field of genome editing. These have been promptly accepted in both the research and commercial industry. On the whole, the widespread use of molecular markers with their types, their appliance in plant breeding along with the advances in genetic selection and genome editing together being a novel strategy to boost crop yield has been reviewed. [ABSTRACT FROM AUTHOR]