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Knowing the genes involved in quantitative traits provides an entry point to understanding the biological bases of behavior, but there are very few examples where the pathway from genetic locus to behavioral change is known. To explore the role of specific genes in fear behavior, we mapped three fear-related traits, tested fourteen genes at six quantitative trait loci (QTLs) by quantitative complementation, and identified six genes. Four genes, Lamp, Ptprd, Nptx2, and Sh3gl, have known roles in synapse function; the fifth, Psip1, was not previously implicated in behavior; and the sixth is a long non-coding RNA, 4933413L06Rik, of unknown function. Variation in transcriptome and epigenetic modalities occurred preferentially in excitatory neurons, suggesting that genetic variation is more permissible in excitatory than inhibitory neuronal circuits. Our results relieve a bottleneck in using genetic mapping of QTLs to uncover biology underlying behavior and prompt a reconsideration of expected relationships between genetic and functional variation.

Pod quality and yield traits in snap bean (Phaseolus vulgaris L.) influence consumer preferences, crop adoption by farmers, and the ability of the product to be commercially competitive locally and globally. The objective of the study was to identify the quantitative trait loci (QTL) for pod quality and yield traits in a snap × dry bean recombinant inbred line (RIL) population. A total of 184 F6 RILs derived from a cross between Vanilla (snap bean) and MCM5001 (dry bean) were grown in three field sites in Kenya and one greenhouse environment in Davis, CA, USA. They were genotyped at 5,951 single nucleotide polymorphisms (SNPs), and composite interval mapping was conducted to identify QTL for 16 pod quality and yield traits, including pod wall fiber, pod string, pod size, and harvest metrics. A combined total of 44 QTL were identified in field and greenhouse trials. The QTL for pod quality were identified on chromosomes Pv01, Pv02, Pv03, Pv04, Pv06, and Pv07, and for pod yield were identified on Pv08. Co-localization of QTL was observed for pod quality and yield traits. Some identified QTL overlapped with previously mapped QTL for pod quality and yield traits, with several others identified as novel. The identified QTL can be used in future marker-assisted selection in snap bean.

Summary DNA methylation is an essential epigenetic modification for gene regulation in plant growth and development. However, the precise mechanisms of DNA methylation remain poorly understood, especially in woody plants. We employed whole‐genome bisulfite sequencing (WGBS), assays for transposase‐accessible chromatin using sequencing (ATAC‐seq), and RNA‐Seq to investigate epigenetic regulatory relationships in Populus tomentosa treated with DNA methylation inhibitor 5‐azacitidine. Expression‐quantitative trait methylation analysis (eQTM), epigenome‐wide association study (EWAS), and joint linkage‐linkage disequilibrium mapping were used to explore the epigenetic regulatory genes, and using CRISPR/Cas9 to identify the role of candidate genes. Plant developmental abnormalities occurred when DNA methylation levels were substantially reduced. DNA methylation regulated 112 expressed genes via chromatin accessibility, of which 61 genes were significantly influenced by DNA methylation variation at the population level. One DNA methylation‐regulated gene, PtoGntK, was located in a major quantitative trait locus (QTL) for poplar growth. Overexpression and CRISPR/Cas9 of PtoGntK revealed it affected poplar height and stem diameter. The PtoRAP2.12 was found to bind to the demethylated accessible region in the PtoGntK promoter, thereby promoting growth in poplar. This study identified key genes with epigenetic regulation for plant growth and provides insights into epigenetic regulation mechanisms in woody plants. [ABSTRACT FROM AUTHOR]

Ethanol stress in Saccharomyces cerevisiae is a well-studied phenomenon, but pinpointing specific genes or polymorphisms governing ethanol tolerance remains a subject of ongoing debate. Naturally found in sugar-rich environments, this yeast has evolved to withstand high ethanol concentrations, primarily produced during fermentation in the presence of suitable oxygen or sugar levels. Originally a defense mechanism against competing microorganisms, yeast-produced ethanol is now a cornerstone of brewing and bioethanol industries, where customized yeasts require high ethanol resistance for economic viability. However, yeast strains exhibit varying degrees of ethanol tolerance, ranging from 8 to 20%, making the genetic architecture of this trait complex and challenging to decipher. In this study, we introduce a novel QTL mapping pipeline to investigate the genetic markers underlying ethanol tolerance in an industrial bioethanol S. cerevisiae strain. By calculating missense mutation frequency in an allele located in a prominent QTL region within a population of 1011 S. cerevisiae strains, we uncovered rare occurrences in gene IRA2. Following molecular validation, we confirmed the significant contribution of this gene to ethanol tolerance, particularly in concentrations exceeding 12% of ethanol. IRA2 pivotal role in stress tolerance due to its participation in the Ras-cAMP pathway was further supported by its involvement in other tolerance responses, including thermotolerance, low pH tolerance, and resistance to acetic acid. Understanding the genetic basis of ethanol stress in S. cerevisiae holds promise for developing robust yeast strains tailored for industrial applications. [ABSTRACT FROM AUTHOR]

ABSTRACT Dwarfing genes that are considerably reducing plant height are used in many cereals. In triticale, the rye‐derived dominant dwarfing gene Ddw1 was introgressed in commercial varieties. It has already been shown that this gene increases Fusarium head blight (FHB) susceptibility in one segregating population. We aimed for verifying this effect in the genetically unrelated doubled haploid (DH) population Cando (Ddw1) × Tritikon (ddw1), with 182 progenies in an experiment with artificial inoculation across six location–year combinations (environments). Linkage mapping was performed with DArTseq markers. The progenies significantly (p < 0.001) varied for FHB severity, plant height and heading stage with high entry‐mean heritabilities (0.85–0.98). The population showed a bimodal distribution for plant height. A significant QTL on chromosome 5RL was found for all three traits explaining 38%, 62% and 43% of the genotypic variation for FHB severity, plant height and heading stage, respectively, and most likely representing Ddw1. This gene increased FHB severity by 5.6 percentage points, delayed heading by 2.7 EC stages and reduced plant height by 29.6 cm on average. To use this gene in practical triticale breeding, the genetic background must be enriched with FHB resistance QTL to counterbalance the negative effect of Ddw1 either by introgression of major FHB QTL from exotic sources or by genomic selection within the adapted gene pool. [ABSTRACT FROM AUTHOR]

BACKGROUND RESULTS CONCLUSION Yellow mosaic disease (YMD) is the most devastating disease of soybean under north Indian conditions. A recombinant inbred line population derived from SL 958 (R) × AGS 456 (S) was used to map the genes imparting YMD resistance. Genotyping by sequencing (GBS) of 148 individuals and the parents was used to identify polymorphic SNPs in the population. These were used to generate linkage maps and subsequently map the QTL.A QTL, MYMIV 1‐1.1, was mapped onto chromosome 6. The QTL was mapped at a genetic distance of 114.31 cM, with likelihood ratio of 81.34 (LOD 17.68), explaining 33.80% of the variation for the trait, with an additive effect of 1.22. MYMIV 1‐1.1 was flanked by SNPs Gm06_12614920 explaining 33.80% of variation and Gm06_12887789 explaining 31.04% of the variation. The QTL region spanned for a total of 2.798 Mbp.The QTL was mapped in an approximately 4 cM region. Flanking SNPs can be developed into linked markers for effective marker‐assisted selection. Out of the genes in the QTL region, Glyma.06G161700 (Suppressor of Gene Silencing/SGS3) is the strongest contender for the resistance gene. This is the first study documenting GBS‐based mapping of YMD resistance in soybean. © 2024 Society of Chemical Industry. [ABSTRACT FROM AUTHOR]

Disease outbreaks in aquaculture have recently intensified. In particular, visceral white-nodules disease, caused by Pseudomonas plecoglossicida, has severely hindered the small yellow croaker (Larimichthys polyactis) aquaculture industry. However, research on this disease is limited. To address this gap, the present study employed a 100K SNP chip to genotype individuals from an F1 full-sib family, identify single nucleotide polymorphisms (SNPs), and construct a genetic linkage map for this species. A high-density genetic linkage map spanning a total length of 1395.72 cM with an average interval of 0.08 cM distributed across 24 linkage groups was obtained. Employing post-infection survival time as an indicator of disease resistance, 13 disease resistance-related quantitative trait loci (QTLs) were detected, and these regions included 169 genes. Functional enrichment analyses pinpointed 11 candidate disease resistance-related genes. RT-qPCR analysis revealed that the genes of chmp1a and arg1 are significantly differentially expressed in response to P. plecoglossicida infection in spleen and liver tissues, indicating their pivotal functions in disease resistance. In summary, in addition to successfully constructing a high-density genetic linkage map, this study reports the first QTL mapping for visceral white-nodules disease resistance. These results provide insight into the intricate molecular mechanisms underlying disease resistance in the small yellow croaker. [ABSTRACT FROM AUTHOR]

Sesame (Sesamum indicum L.) is an important oilseed crop widely cultivated in subtropical and tropical areas. Low genetic yield potential and susceptibility to disease contribute to low productivity in sesame. However, the genetic basis of sesame yield- and disease-related traits remains unclear. Here, we represent the construction of a high-density bin map of sesame using whole genome sequencing of an F2 population derived from 'Yizhi' and 'Mingdeng Zhima'. A total of 2766 Bins were categorized into 13 linkage groups. Thirteen significant QTLs were identified, including ten QTLs related to yield, two QTLs related to Sesame Fusarium wilt (SFW) disease, and one QTL related to seed color. Among these QTLs, we found that SFW-QTL1.1 and SFW-QTL1.2 were major QTLs related to Fusarium wilt disease, explaining more than 20% of the phenotypic variation with LOD > 6. SCC-QTL1.1 was related to seed coat color, explaining 52% of the phenotypic variation with LOD equal to 25.3. This suggests that seed color traits were controlled by a major QTL. Candidate genes related to Fusarium wilt disease and seed color in the QTLs were annotated. We discovered a significant enrichment of genes associated with resistance to late blight. These genes could be spectral disease resistance genes and may have a role in the regulation of Fusarium wilt disease resistance. Our study will benefit the implementation of marker-assisted selection (MAS) for the genetic improvement of disease resistance and yield-related traits in sesame. [ABSTRACT FROM AUTHOR]

Summary: Developing early maturing lentil has the potential to minimize yield losses, mainly during terminal drought. Whole‐genome resequencing (WGRS) based QTL‐seq identified the loci governing earliness in lentil. The genetic analysis for maturity duration provided a good fit to 3:1 segregation (F2), indicating earliness as a recessive trait. WGRS of Globe Mutant (late parent), late‐flowering, and early‐flowering bulks (from RILs) has generated 1124.57, 1052.24 million raw and clean reads, respectively. The QTL‐Seq identified three QTLs (LcqDTF3.1, LcqDTF3.2, and LcqDTF3.3) on chromosome 3 having 246244 SNPs and 15577 insertions/deletions (InDels) and 13 flowering pathway genes. Of these, 11 exhibited sequence variations between bulks and validation (qPCR) revealed a significant difference in the expression of nine candidate genes (LcGA20oxG, LcFRI, LcLFY, LcSPL13a, Lcu.2RBY.3g060720, Lcu.2RBY.3g062540, Lcu.2RBY.3g062760, LcELF3a, and LcEMF1). Interestingly, the LcELF3a gene showed significantly higher expression in late‐flowering genotype and exhibited substantial involvement in promoting lateness. Subsequently, an InDel marker (I‐SP‐383.9; LcELF3a gene) developed from LcqDTF3.2 QTL region showed 82.35% PVE (phenotypic variation explained) for earliness. The cloning, sequencing, and comparative analysis of the LcELF3a gene from both parents revealed 23 SNPs and InDels. Interestingly, a 52 bp deletion was recorded in the LcELF3a gene of L4775, predicted to cause premature termination of protein synthesis after 4 missense amino acids beyond the 351st amino acid due to the frameshift during translation. The identified InDel marker holds significant potential for breeding early maturing lentil varieties. [ABSTRACT FROM AUTHOR]

Late blight (LB), caused by oomycete Phytophthora infestans, is one of the most destructive diseases of the cultivated tomato, Solanum lycopersicum. Since new and aggressive clonal lineages of P. infestans, many of which overcoming formerly effective fungicides or host resistance genes, have continued to emerge, it is crucial to identify, characterize, and utilize new sources of host resistance in tomato breeding. A recent screening of tomato germplasm identified Solanum pimpinellifolium accession PI 224710 with very strong resistance to several current P. infestans clonal lineages. The present study aimed to identify and characterize QTLs associated with LB resistance in PI 224710. Disease screening of a large F2 population (n = 1721), derived from a cross between PI 224710 and LB-susceptible tomato breeding line Fla. 8059, followed by F3 progeny testing, resulted in the identification of 43 highly-resistant and 27 highly-susceptible F2 individuals. A selective genotyping approach, using 469 non-identical SNP markers, resulted in the construction of a genetic linkage map and identification of three LB-resistance QTLs on chromosomes 6, 9 and 10 of PI 224710. A comparison of the QTLs genomic locations with the tomato physical map resulted in the identification of several candidate genes, which might be underpinning the LB-resistance QTLs in PI 224710. The identified markers associated with the LB-resistance QTLs can be utilized in breeding programs to transfer resistance from PI 224710 into tomato breeding lines and hybrid cultivars via marker-assisted breeding; they also can be used to develop near-isogenic lines for fine mapping of the QTLs. [ABSTRACT FROM AUTHOR]

Rice grain number is a crucial agronomic trait impacting yield. In this study, we characterized a quantitative trait locus (QTL), GRAIN NUMBER 1.1 (GN1.1), which encodes a Flowering Locus T‐like1 (FT‐L1) protein and acts as a negative regulator of grain number in rice. The elite allele GN1.1B, derived from the Oryza indica variety, BF3‐104, exhibits a 14.6% increase in grain yield compared with the O. japonica variety, Nipponbare, based on plot yield tests. We demonstrated that GN1.1 interacted with and enhanced the stability of ADP‐ribosylation factor (Arf)‐GTPase‐activating protein (Gap), OsZAC. Loss of function of OsZAC results in increased grain number. Based on our data, we propose that GN1.1B facilitates the elevation of auxin content in young rice panicles by affecting polar auxin transport (PAT) through interaction with OsZAC. Our study unveils the pivotal role of the GN1.1 locus in rice panicle development and presents a novel, promising allele for enhancing rice grain yield through genetic improvement. [ABSTRACT FROM AUTHOR]

The continuous emergence of new Puccinia striiformis Westend f. sp. tritici Erikss (Pst) races requires a sustained search for useful sources of resistance. A CIMMYT bread wheat line (pedigree: Milan/S87230//Babax; renamed NSRPan4) was identified as highly resistant to South African Pst races. A recombinant inbred line (RIL) mapping population was developed by crossing NSRPan4 with Avocet S. Stripe rust data collected for RILs, using Pst race 6E22A + , include seedling infection types determined under controlled conditions as well as adult plant responses determined in field trials over three consecutive seasons. Quantitative trait loci (QTL) mapping identified stripe rust resistance genes/QTL on chromosomes 2A and 2B, temporarily designated as QYr.ufs-2A.2(YR17) and QYr.ufs-2B.1, respectively. The QTL interval on chromosome 2A, which includes the LR37/YR17/SR38 gene complex (also referred to as the 2NS/2AS or 2NVS segment), conferred a significant seedling (R2 23.5%) and adult plant resistance effect (R2 up to 54.5%). The QTL on 2B contributed up to 46.4% of phenotypic variance observed. Three minor QTL, temporarily designated as QYr.ufs-1B.1 (possibly LR46/YR29), QYr.ufs-3D.1 and QYr.ufs-7A.1 were also detected. Our results support findings that notwithstanding the reported virulence for YR17, the LR37/YR17/SR38 segment remains useful in combination with other sources of resistance in certain genetic backgrounds and environments. Together with QYr.ufs-2B.1 and in the presence of the detected minor QTL and yet unidentified resistances, it was a consistent major contributor to the high level of stripe rust resistance in NSRPan4 to South African races of Pst. [ABSTRACT FROM AUTHOR]

The first step in trait introgression is to identify and assess novel sources of variation. For shrub willow (Salix) breeders, there is an abundance of understudied species within a genus that readily hybridizes. Breeding targets in shrub willow center on traits contributing to biomass yield for bioenergy. These include stem biomass, insect and pathogen resistance, and leaf architecture traits. More specifically, breeding for durable resistance to willow leaf rust (Melampsora spp.) is of particular importance as the pathogen can significantly reduce biomass yields in commercial production. The Salix F1 hybrid common parent population (Salix F1 HCP) was created to characterize the variation among eight species‐hybrid families and map QTL for targeted traits. A female and male S. purpurea were used as common parents in crosses made to male S. suchowensis, S. viminalis, S. koriyanagi, and S. udensis and female S. viminalis, S. integra, S. suchowensis to produce eight families that were planted in field trials at Cornell AgriTech in Geneva, NY and phenotyped. Using 16 previously described parental backcross linkage maps and two newly generated S. purpurea consensus maps, we identified 215 QTL across all eight families and in every parent. These included 15 leaf rust severity, 61 herbivory, 65 leaf architecture, and 74 yield component QTL, resulting in 50 unique overlapping regions within the population. These genetic loci serve as an important foundation for future shrub willow breeding, and each interspecific family was identified as a novel source of useful alleles for trait introgression into high yielding cultivars. [ABSTRACT FROM AUTHOR]

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]

During the process of almond (Prunus dulcis) domestication, essential traits, which gave plants the plasticity for facing unstable environmental conditions, were lost. In general, the domestication process often narrows the natural genetic diversity. Modern selections (i.e., breeding programs) dramatically accelerated this genetic bottleneck trend to a few successful almond cultivars, which are presently the founders of most commercial cultivars worldwide. The concept of utilizing wild species as a source for important traits and for the enrichment of the gene pool was deeply discussed in previous studies. However, in almonds and other Prunus species, deliberate utilization of wild species as a genetic resource for breeding programs is quite rare. To address these significant challenges, we generated an interspecific F1 population between the Israeli almond cultivar Um el Fahem (UEF) and a specimen of a local wild almond species, Prunus arabica (P. arabica), originating from the Judea desert. This interspecific F1 population possesses high phenotypic variability, and sixteen segregating traits were phenotyped. Among the segregating traits, we were able to genetically associate six agriculturally important traits, such as leaf chlorophyll content (LCC), flower size, and fruit size. The alleles for Self-Compatibility (SC) and kernel bitterness were previously mapped in almond and were reexamined on the background of the distinctive wild genetic material of P. arabica. Finally, phenotypic interactions between traits were suggested, such as rootstock perimeter and canopy area that were positively correlated with total yield in the F1 population. This study is a first step towards developing a well-characterized almond interspecies genetic population. The availability of such a genetic tool with detailed phenotypic analysis is crucial to address and explore the profound influence of almond wild species in Prunus genetic research and breeding. By using the interspecific population as the infrastructure, we show the advantages and importance of utilizing wild relatives. [ABSTRACT FROM AUTHOR]

Eastern black walnut, Juglans nigra L., is an economically important tree species valued for its high-quality timber and edible nuts. A regional industry for the species' nut and kernel products resides in Missouri, where over 9 million kg of hulled in-shell nuts are purchased in masting years. The crop is primarily based upon nuts harvested from wild trees, placing a ceiling on nut volume and quality (e.g. small nut size, dark pellicle color, and 10–14% kernel by weight). Orchards of named cultivars, like 'Kwik Krop' and 'Sparrow', supply up to 22,000 kg of nuts with a higher kernel percentage (> 26%) and improved quality. Such cultivars often represent chance wild or on-farm seedlings, clonally propagated since the late 1800's by enthusiasts. Today, continued improvement of eastern black walnut as an orchard crop is limited by a long generation time, delayed expression of important traits, and space requirements – creating a strong need for marker-trait association studies that inform progeny selection. The first linkage map for J. nigra was recently created using the 'Sparrow' × 'Schessler' F1 population and loci for phenology traits discovered. The objective of this study is to utilize these genetic resources to detect quantitative trait loci (QTL) and report associated DNA markers for the spur-bearing habit, which promotes precocity and high yield. Using single-year data from the 11-year-old population, we observe that segregation for the spur-bearing habit appears to be recessive and multigenic. Three QTLs (p > 0.99) were identified on linkage group (LG) 8, LG11, and LG16 that explain 7.2%, 8.7%, and 10% of trait variation, respectively. Regions between flanking DNA markers were 3.16 cM, 4.32 cM, and 9.69 cM, respectively. This study is the first to examine the genetic control of bearing habit and yield in eastern black walnut and informs breeders' approach for their future genetic improvement. [ABSTRACT FROM AUTHOR]

Goji berries are a small-fruited shrub with industrial importance whose fruit considered beneficial in both fresh and dried forms. Current germplasms of goji berries include small fruits with a short shelf life, less sweet and bitter taste, and a lack of appropriate genetic information. This study aimed to employ whole genome resequencing to generate an ultra-dense bin linkage map and to elucidate the genetic basis of goji fruit quality and size using quantitative trait loci (QTL) mapping analysis in a cross-pollinated hybrid population. To achieve this goal, human sensory tests were carried out to determine the bitter taste (BT) and sweet taste (ST), and to quantify the soluble solid content (SSC), fruit firmness (FF), and fruit size-related traits of fresh goji fruits over three or four years. The results revealed that the goji bin linkage map based on resequencing spanned a total length of 966.42 cM and an average bin interval of 0.03 cM. Subsequent variant calling and ordering resulted in 3,058 bins containing 35,331 polymorphic markers across 12 chromosomes. A total of 99 QTLs, with individual loci in different environments explaining a phenotypic variance of 1.21-16.95% were identified for the studied traits. Ten major effects, including colocalized QTLs corresponding to different traits, were identified on chromosomes 1, 3, 5, 6, 7, and 8, with a maximum Logarithm of Odds (LOD) of 29.25 and 16.95% of explained phenotypic variance (PVE). In addition, four stable loci, one for FF, one for fruit weight (FW), and two for fruit shape index (FSI), were mainly mapped on chromosomes 5, 6, and 7, elucidating 2.10-16.95% PVE. These findings offer valuable insights into the genetic architecture of goji fruit traits along with identified specific loci and markers to further improve and develop sweeter, less bitter and larger fruited goji berry cultivars with extended shelf life. [ABSTRACT FROM AUTHOR]

How the timing of development is linked to organismal size is a longstanding question. Although numerous studies have reported a correlation of temporal and spatial traits, the developmental or selective constraints underlying this link remain largely unexplored. We address this question by studying the periodic process of embryonic axis segmentation in-vivo in Oryzias fish. Interspecies comparisons reveal that the timing of segmentation correlates to segment, tissue and organismal size. Segment size in turn scales according to tissue and organism size. To probe for underlying causes, we genetically hybridised two closely related species. Quantitative analysis in ~600 phenotypically diverse F2 embryos reveals a decoupling of timing from size control, while spatial scaling is preserved. Using developmental quantitative trait loci (dev QTL) mapping we identify distinct genetic loci linked to either the control of segmentation timing or tissue size. This study demonstrates that a developmental constraint mechanism underlies spatial scaling of axis segmentation, while its spatial and temporal control are dissociable modules. Synopsis: The molecular relationships that link developmental timing and organismal size remain underexplored. Here, a cross-species analysis in Oryzias fish measures the timing of embryonic body axis segmentation and overall organismal size, providing evidence that timing and size control are dissociable modules. Real-time imaging of the segmentation clock in F2 embryos from interspecies crosses of Oryzias fish reveals a broad phenotypic spectrum. F2 embryos exhibit a linear relationship between PSM and somite size, indicating that a developmental constraint mechanism underlies spatial scaling. developmental quantitative trait loci (dev QTL) analysis of F2 embryos identifies distinct genomic loci correlated with segmentation timing and tissue size, respectively. Interspecies comparison in rice fish (Orzyias spp.) shows that both the rate and size of embryonic segmentation increase in proportion to fish size but are regulated by independent mechanisms. [ABSTRACT FROM AUTHOR]

Background: Phenotyping of plant traits presents a significant bottleneck in Quantitative Trait Loci (QTL) mapping and genome-wide association studies (GWAS). Computerized phenotyping using digital images promises rapid, robust, and reproducible measurements of dimension, shape, and color traits of plant organs, including grain, leaf, and floral traits. Results: We introduce GRABSEEDS, which is specifically tailored to extract a comprehensive set of features from plant images based on state-of-the-art computer vision and deep learning methods. This command-line enabled tool, which is adept at managing varying light conditions, background disturbances, and overlapping objects, uses digital images to measure plant organ characteristics accurately and efficiently. GRABSEED has advanced features including label recognition and color correction in a batch setting. Conclusion: GRABSEEDS streamlines the plant phenotyping process and is effective in a variety of seed, floral and leaf trait studies for association with agronomic traits and stress conditions. Source code and documentations for GRABSEEDS are available at: https://github.com/tanghaibao/jcvi/wiki/GRABSEEDS. [ABSTRACT FROM AUTHOR]

Introduction: Owing to advances in high-throughput genome sequencing, QTLSeq mapping of salt tolerance traits is a major platform for identifying soil-salinity tolerance QTLs to accelerate marker-assisted selection for salt-tolerant rice varieties. We performed QTL-BSA-Seq in the seedling stage of rice from a genetic cross of the extreme salt-sensitive variety, IR29, and "Jao Khao" (JK), a Thai salt-tolerant variety. Methods: A total of 462 F2 progeny grown in soil and treated with 160 mM NaCl were used as the QTL mapping population. Two high- and low-bulk sets, based on cell membrane stability (CMS) and tiller number at the recovery stage (TN), were equally sampled. The genomes of each pool were sequenced, and statistical significance of QTL was calculated using QTLseq and G prime (G') analysis, which is based on calculating the allele frequency differences or D(SNP index). Results: Both methods detected the overlapping interval region, wherein CMSbulk was mapped at two loci in the 38.41-38.85 Mb region with 336 SNPs on chromosome 1 (qCMS1) and the 26.13-26.80 Mb region with 1,011 SNPs on chromosome 3 (qCMS3); the D(SNP index) peaks were -0.2709 and 0.3127, respectively. TN-bulk was mapped at only one locus in the overlapping 38.26-38.95 Mb region on chromosome 1 with 575 SNPs (qTN1) and a D(SNP index) peak of -0.3544. These identified QTLs in two different genetic backgrounds of segregating populations derived from JK were validated. The results confirmed the colocalization of the qCMS1 and qTN1 traits on chromosome 1. Based on the CMS trait, qCMS1/qTN1 stably expressed 6%-18% of the phenotypic variance in the two validation populations, while qCMS1/qTN1 accounted for 16%-20% of the phenotypic variance in one validation population based on the TN trait. Conclusion: The findings confirm that the CMS and TN traits are tightly linked to the long arm of chromosome 1 rather than to chromosome 3. The validated qCMS-TN1 QTL can be used for gene/QTL pyramiding in marker-assisted selection to expedite breeding for salt resistance in rice at the seedling stage. [ABSTRACT FROM AUTHOR]

Candidate genes related to first pod height (FPH) traits in faba bean plants are crucial for mechanised breeding. However, reports on quantitative trait locus (QTL) mapping related to the FPH of faba bean are few, thus limiting the high-quality development of the faba bean industry to a certain extent. The identification and screening of candidate genes related to FPH is extremely urgent for the advancement of mechanised breeding for faba bean. In this study, a high-density genetic linkage map was constructed using genotyping-by-sequencing (GBS) of an F3 population and QTLs (genes) related to FPH were identified. The genetic linkage map contained seven linkage groups with 3012 SNP markers with an overall length of 4089.13 centimorgan (cM) and an average marker density of 1.36 cM. Thirty-eight QTLs for the first pod node (FPN) and FPH were identified (19 each for FPN and FPH). The 19 QTLs associated with FPN were located on chromosomes 1L, 1S, 2, 3, 4, 5, and 6; the 19 QTLs associated with FPH were located on chromosomes 1L, 1S, 2, 3, 5, and 6. There was a co-localisation interval of qFPN6-1 and qFPH6-1 on chromosome 6. By annotating the QTL qFPH6-1 interval, 36 genes that may be related to FPH were identified, these genes are related to plant growth and development. The results provide a basis for the precise location of QTLs related to FPH and could accelerate the breeding of faba bean varieties adapted to mechanised harvesting. [ABSTRACT FROM AUTHOR]

Leaf angle (LA) is closely related to plant architecture, photosynthesis and density tolerance in maize. In the current study, we used a recombinant inbred line population constructed by two maize-inbred lines to detect quantitative trait loci (QTLs) controlling LA. Based on the average LA in three environments, 13 QTLs were detected, with the logarithm of odds ranging from 2.7 to 7.21, and the phenotypic variation explained by a single QTL ranged from 3.93% to 12.64%. A stable QTL, qLA2-3, on chromosome 2 was detected and was considered to be the major QTL controlling the LA. On the basis of verifying the genetic effect of qLA2-3, a fine map was used to narrow the candidate interval, and finally, the target segment was located at a physical distance of approximately 338.46 kb (B73 RefGen_v4 version), containing 16 genes. Re-sequencing and transcriptome results revealed that five candidate genes may be involved in the regulation of LA. The results enrich the information for molecular marker-assisted selection of maize LA and provide genetic resources for the breeding of dense planting varieties. [ABSTRACT FROM AUTHOR]

Leaf angle (LA) is an important trait of plant architecture, and individuals with narrow LA can better capture canopy light under high-density planting, which is beneficial for increasing the overall yield per unit area. To study the genetic basis and molecular regulation mechanism of leaf angle in rapeseed, we carried out a series of experiments. Quantitative trait loci (QTL) mapping was performed using the RIL population, and seven QTLs were identified. Transcriptome analysis showed that the cell wall formation/biogenesis processes and biosynthesis/metabolism of cell wall components were the most enrichment classes. Most differentially expressed genes (DEGs) involved in the synthesis of lignin, xylan, and cellulose showed down-regulated expression in narrow leaf material. Microscopic analysis suggested that the cell size affected by the cell wall in the junction area of the stem and petiole was the main factor in leaf petiole angle (LPA) differences. Combining QTL mapping and RNA sequencing, five promising candidate genes BnaA01G0125600ZS, BnaA01G0135700ZS, BnaA01G0154600ZS, BnaA10G0154200ZS, and BnaC03G0294200ZS were identified in rapeseed, and most of them were involved in cell wall biogenesis and the synthesis/metabolism of cell wall components. The results of QTL, transcriptome analysis, and cytological analysis were highly consistent, collectively revealing that genes related to cell wall function played a crucial role in regulating the LA trait in rapeseed. The study provides further insights into LA traits, and the discovery of new QTLs and candidate genes is highly beneficial for genetic improvement. [ABSTRACT FROM AUTHOR]

Starch is the main component that determines the yield and quality of Tartary buckwheat. As a quantitative trait, using quantitative trait locus (QTL) mapping to excavate genes associated with starch-related traits is crucial for understanding the genetic mechanisms involved in starch synthesis and molecular breeding of Tartary buckwheat varieties with high-quality starch. Employing a recombinant inbred line population as research material, this study used QTL mapping to investigate the amylose, amylopectin, and total starch contents across four distinct environments. The results identified a total of 20 QTLs spanning six chromosomes, which explained 4.07% to 14.41% of the phenotypic variation. One major QTL cluster containing three stable QTLs governing both amylose and amylopectin content, qClu-4-1, was identified and located in the physical interval of 39.85–43.34 Mbp on chromosome Ft4. Within this cluster, we predicted 239 candidate genes and analyzed their SNP/InDel mutations, expression patterns, and enriched KEGG pathways. Ultimately, five key candidate genes, namely FtPinG0004897100.01, FtPinG0002636200.01, FtPinG0009329200.01, FtPinG0007371600.01, and FtPinG0005109900.01, were highlighted, which are potentially involved in starch synthesis and regulation, paving the way for further investigative studies. This study, for the first time, utilized QTL mapping to detect major QTLs controlling amylose, amylopectin, and total starch contents in Tartary buckwheat. The QTLs and candidate genes would provide valuable insights into the genetic mechanisms underlying starch synthesis and improving starch-related traits of Tartary buckwheat. [ABSTRACT FROM AUTHOR]

High-quality genetic maps are effective tools for elucidating the genetic mechanisms of complex quantitative traits and facilitating marker-assisted breeding. Species within the genus Liquidambar (commonly called sweetgum), particularly Liquidambar styraciflua and Liquidambar formosana, are significant forest resources worldwide. These sweetgum trees have been extensively utilized in medical and cosmetic applications for centuries as they contain large amounts of valuable secondary metabolites. Among these, shikimic acid is a notable metabolite with significant pharmaceutical applications. Despite advances in conventional breeding and propagation techniques for sweetgum, the genetic basis and regulatory mechanisms of valuable traits remain largely unexplored. In this study, we constructed the first high-density genetic map for sweetgum using whole-genome resequencing (WGR) of 220 progeny individuals derived from a cross of L. styraciflua × L. formosana. The genetic map spanned a total distance of 1428.51 centimorgans (cM) with an average inter-marker distance of 0.33 cM, incorporating 4268 bin markers across 16 linkage groups. To identify the genetic loci controlling the shikimic acid content, quantitative trait locus (QTL) mapping was carried out based on the genetic map. Two QTLs located on linkage group (LG) 12 were detected, encompassing a total of 213 genes within the QTL interval. Some of these genes are closely related to secondary metabolism in plants, including YUCCA and DXS genes. This study presents the first high-quality genetic map of sweetgum and provides a preliminary QTL analysis for shikimic acid content. Our findings establish a foundational framework for the genetic improvement of sweetgum through marker-assisted breeding and offer valuable insights for further research in sweetgum genetics. [ABSTRACT FROM AUTHOR]

The size of peanut pods and seeds, which directly affects yield and quality, also has significant implications for mechanized production and market efficiency. Identifying relevant loci and mining candidate genes is crucial for cultivating high-yield peanut varieties. In this study, we employed advanced generation recombinant inbred lines developed by crossbreeding Huayu 44 and DF12 as the experimental material. Quantitative trait locus (QTL) mapping for traits related to pod and seed size was conducted across six environments. A total of 44 QTLs were detected, distributed on chromosomes A02, A05, B04, B08, and B10. An enrichment region for multiple QTLs was also identified on chromosome A05 (19.28~52.32 cm). In this region, 10 KASP markers were developed, narrowing the enrichment area to two candidate gene hotspot regions of 600.9 kb and 721.2 kb. By combining gene prediction and functional annotation within the intervals, 10 candidate genes, including those encoding cytochrome P450 protein, polyamine synthase, mannose-1-phosphate guanylyltransferase, pentatricopeptide repeat protein, and E2F transcription factor, were identified as regulators of pod and seed size. This study provides technical support for the genetic improvement and key gene identification of peanut pod and seed size. [ABSTRACT FROM AUTHOR]

Cotton breeding for the development of early-maturing varieties is an effective way to improve multiple cropping indexes and alleviate the conflict between grains and cotton in the cultivated fields in China. In the present study, we aimed to identify upland cotton quantitative trait loci (QTLs) and candidate genes related to early-maturity traits, including whole growth period (WGP), flowering timing (FT), node of the first fruiting branch (NFFB), height of the node of the first fruiting branch (HNFFB), and plant height (PH). An early-maturing variety, CCRI50, and a late-maturing variety, Guoxinmian 11, were crossed to obtain biparental populations. These populations were used to map QTLs for the early-maturity traits for two years (2020 and 2021). With BSA-seq analysis based on the data of population 2020, the candidate regions related to early maturity were found to be located on chromosome D03. We then developed 22 polymorphic insertions or deletions (InDel) markers to further narrow down the candidate regions, resulting in the detection of five and four QTLs in the 2020 and 2021 populations, respectively. According to the results of QTL mapping, two candidate regions (InDel_G286-InDel_G144 and InDel_G24-InDel_G43) were detected. In these regions, three genes (GH_D03G0451, GH_D03G0649, and GH_D03G1180) have non-synonymous mutations in their exons and one gene (GH_D03G0450) has SNP variations in the upstream sequence between CCRI50 and Guoxinmian 11. These four genes also showed dominant expression in the floral organs. The expression levels of GH_D03G0451, GH_D03G0649 and GH_D03G1180 were significantly higher in CCRI50 than in Guoxinmian 11 during the bud differentiation stages, while GH_D03G0450 showed the opposite trend. Further functional verification of GH_D03G0451 indicated that the GH_D03G0451-silenced plants showed a delay in the flowering time. The results suggest that these are the candidate genes for cotton early maturity, and they may be used for breeding early-maturity cotton varieties.

Seed size is an important agronomic trait in melons that directly affects seed germination and subsequent seedling growth. However, the genetic mechanism underlying seed size in melon remains unclear. In the present study, we employed Bulked-Segregant Analysis sequencing (BSA-seq) to identify a candidate region (~1.35 Mb) on chromosome 6 that corresponds to seed size. This interval was confirmed by QTL mapping of three seed size-related traits from an F2 population across three environments. This mapping region represented nine QTLs that shared an overlapping region on chromosome 6, collectively referred to as qSS6.1. New InDel markers were developed in the qSS6.1 region, narrowing it down to a 68.35 kb interval that contains eight annotated genes. Sequence variation analysis of the eight genes identified a SNP with a C to T transition mutation in the promoter region of MELO3C014002, a leucine-rich repeat receptor-like kinase (LRR-RLK) gene. This mutation affected the promoter activity of the MELO3C014002 gene and was successfully used to differentiate the large-seeded accessions (C-allele) from the small-seeded accessions (T-allele). qRT-PCR revealed differential expression of MELO3C014002 between the two parental lines. Its predicted protein has typical LRR-RLK family domains, and phylogenetic analyses reveled its similarity with the homologs in several plant species. Altogether, these findings suggest MELO3C014002 as the most likely candidate gene involved in melon seed size regulation. Our results will be helpful for better understanding the genetic mechanism regulating seed size in melons and for genetically improving this important trait through molecular breeding pathways.

Barley net form net blotch (NFNB) is a destructive foliar disease caused by Pyrenophora teres f. teres. Barley line CIho5791, which harbors the broadly effective chromosome 6H resistance gene Rpt5, displays dominant resistance to P. teres f. teres. To genetically characterize P. teres f. teres avirulence/virulence on the barley line CIho5791, we generated a P. teres f. teres mapping population using a cross between the Moroccan CIho5791-virulent isolate MorSM40-3 and the avirulent reference isolate 0-1. Full genome sequences were generated for 103 progenies. Saturated chromosome-level genetic maps were generated, and quantitative trait locus (QTL) mapping identified two major QTL associated with P. teres f. teres avirulence/virulence on CIho5791. The most significant QTL mapped to chromosome (Ch) 1, where the virulent allele was contributed by MorSM40-3. A second QTL mapped to Ch8; however, this virulent allele was contributed by the avirulent parent 0-1. The Ch1 and Ch8 loci accounted for 27 and 15% of the disease variation, respectively, and the avirulent allele at the Ch1 locus was epistatic over the virulent allele at the Ch8 locus. As a validation, we used a natural P. teres f. teres population in a genome-wide association study that identified the same Ch1 and Ch8 loci. We then generated a new reference quality genome assembly of parental isolate MorSM40-3 with annotation supported by deep transcriptome sequencing of infection time points. The annotation identified candidate genes predicted to encode small, secreted proteins, one or more of which are likely responsible for overcoming the CIho5791 resistance. [Figure: see text] The author(s) have dedicated the work to the public domain under the Creative Commons CC0 “No Rights Reserved” license by waiving all of his or her rights to the work worldwide under copyright law, including all related and neighboring rights, to the extent allowed by law, 2024.

Abstract Background Phenotyping of plant traits presents a significant bottleneck in Quantitative Trait Loci (QTL) mapping and genome-wide association studies (GWAS). Computerized phenotyping using digital images promises rapid, robust, and reproducible measurements of dimension, shape, and color traits of plant organs, including grain, leaf, and floral traits. Results We introduce GRABSEEDS, which is specifically tailored to extract a comprehensive set of features from plant images based on state-of-the-art computer vision and deep learning methods. This command-line enabled tool, which is adept at managing varying light conditions, background disturbances, and overlapping objects, uses digital images to measure plant organ characteristics accurately and efficiently. GRABSEED has advanced features including label recognition and color correction in a batch setting. Conclusion GRABSEEDS streamlines the plant phenotyping process and is effective in a variety of seed, floral and leaf trait studies for association with agronomic traits and stress conditions. Source code and documentations for GRABSEEDS are available at: https://github.com/tanghaibao/jcvi/wiki/GRABSEEDS .

Abstract [Objective] The study aims to discover the genetic loci and candidate genes of seed glucosinolate content in Brassica napus, and lay a foundation for the cloning of genes involved in glucosinolate metabolism and improving the breeding of B. napus. [Methods] Using KN DH populations from four different environments as materials, the QTL mapping of seed glucosinolate content and the candidate genes were analyzed. [Results] (1) The variation coefficient of seed glucosinolate content in B. napus was high and stable, which followed the genetic characteristics of quantitative traits. (2) Seven consistent QTLs, including cqGC.A9-5, cqGC.A9-7, cqGC.A9-9, cqGC.C2-9, cqGC.C2-10, cqGC.C9-5 and cqGC.C9-6, were environmentally stable QTLs, of which cqGC.A9-5, cqGC.C2-10, and cqGC.C9-5 were major QTLs. (3) Three candidate genes, including BnaA09g05480D, BnaC09g05620D, and BnaC09g05810D, were identified in the interval of the major QTL cqGC.A9-5 and cqGC.C9-5. Based on their annotation, these candidate genes were involved in the biosynthetic pathway of glucosinolates (the biosynthesis of IAOx and 3-alkyl malic acid) and transport and distribution of glucosinolates. [Conclusion] Seed glucosinolate content in B. napus was quantitative trait. Three major QTLs for seed glucosinolate content were identified, which might be involved in the synthesis of intermediate products and the transport and distribution of glucosinolates.

Abstract Background Rapeseed (Brassica napus L.) is one of the most important oil crops and a wildly cultivated horticultural crop. The petals of B. napus serve to protect the reproductive organs and attract pollinators and tourists. Understanding the genetic basis of petal morphology regulation is necessary for B. napus breeding. Results In the present study, the quantitative trait locus (QTL) analysis for six B. napus petal morphology parameters in a double haploid (DH) population was conducted across six microenvironments. A total of 243 QTLs and five QTL hotspots were observed, including 232 novel QTLs and three novel QTL hotspots. The spatiotemporal transcriptomic analysis of the diversiform petals was also conducted, which indicated that the expression of plant hormone metabolic and cytoskeletal binding protein genes was variant among diversiform petals. Conclusions The integration of QTL and RNA-seq analysis revealed that plant hormones (including cytokinin, auxin, and gibberellin) and cytoskeleton were key regulators of the petal morphology. Subsequently, 61 high-confidence candidate genes of petal morphology regulation were identified, including Bn.SAUR10, Bn.ARF18, Bn.KIR1, Bn.NGA2, Bn.PRF1, and Bn.VLN4. The current study provided novel QTLs and candidate genes for further breeding B. napus varieties with diversiform petals.

Abstract Background Leaf morphology plays a crucial role in photosynthetic efficiency and yield potential in crops. Cigar tobacco plants, which are derived from common tobacco (Nicotiana tabacum L.), possess special leaf characteristics including thin and delicate leaves with few visible veins, making it a good system for studying the genetic basis of leaf morphological characters. Results In this study, GWAS and QTL mapping were simultaneously performed using a natural population containing 185 accessions collected worldwide and an F2 population consisting of 240 individuals, respectively. A total of 26 QTLs related to leaf morphological traits were mapped in the F2 population at three different developmental stages, and some QTL intervals were repeatedly detected for different traits and at different developmental stages. Among the 206 significant SNPs identified in the natural population using GWAS, several associated with the leaf thickness phenotype were co-mapped via QTL mapping. By analyzing linkage disequilibrium and transcriptome data from different tissues combined with gene functional annotations, 7 candidate genes from the co-mapped region were identified as the potential causative genes associated with leaf thickness. Conclusions These results presented a valuable cigar tobacco resource showing the genetic diversity regarding its leaf morphological traits at different developmental stages. It also provides valuable information for novel genes and molecular markers that will be useful for further functional verification and for molecular breeding of leaf morphological traits in crops in the future.

Pod quality and yield traits in snap bean (Phaseolus vulgaris L.) influence consumer preferences, crop adoption by farmers, and the ability of the product to be commercially competitive locally and globally. The objective of the study was to identify the quantitative trait loci (QTL) for pod quality and yield traits in a snap Ã-- dry bean recombinant inbred line (RIL) population. A total of 184 F6 RILs derived from a cross between Vanilla (snap bean) and MCM5001 (dry bean) were grown in three field sites in Kenya and one greenhouse environment in Davis, CA, USA. They were genotyped at 5,951 single nucleotide polymorphisms (SNPs), and composite interval mapping was conducted to identify QTL for 16 pod quality and yield traits, including pod wall fiber, pod string, pod size, and harvest metrics. A combined total of 44 QTL were identified in field and greenhouse trials. The QTL for pod quality were identified on chromosomes Pv01, Pv02, Pv03, Pv04, Pv06, and Pv07, and for pod yield were identified on Pv08. Co-localization of QTL was observed for pod quality and yield traits. Some identified QTL overlapped with previously mapped QTL for pod quality and yield traits, with several others identified as novel. The identified QTL can be used in future marker-assisted selection in snap bean. [ABSTRACT FROM AUTHOR]

The main objective of mapping quantitative trait loci (QTL) and genome-wide association studies (GWAS) is to identify and locate QTLs on the genome. Estimating the sizes of QTL is equally important as identifying the QTLs. The size of a QTL is often measured by the QTL variance, or the proportion of phenotypic variance explained by the QTL, known as the QTL heritability. The reported QTL heritability is biased upward for small-sized QTLs estimated from small samples, especially in GWAS with a very small P -value threshold accommodating to Bonferroni correction for multiple tests. The phenomenon is called the Beavis effect. Methods of correcting the Beavis effect have been developed for additive effect models. Corresponding methods are not available for QTLs with more than one effect, such as QTLs including dominance and other genetic effects. In this study, we developed explicit formulas for estimating the variances and heritability for QTL with multiple effects. We also developed a method to remove nuisance parameters via an annihilator matrix. Finally, biases in estimated QTL variances caused by the Beavis effect are investigated and corrected. The new method is demonstrated by analyzing the 1000 grain weight (KGW) trait in a hybrid rice population. [ABSTRACT FROM AUTHOR]

Superior fiber quality is one of the most important objectives in cotton breeding. To detect the genetic basis underlying fiber quality, an F2 population containing 413 plants was constructed by crossing Jifeng 914 and Jifeng 173, both of which have superior fiber quality, with Jifeng 173 being better. Five fiber quality traits were investigated in the F2, F2:3, F2:4, and F2:5 populations. Quantitative trait loci (QTL) mapping was conducted based on a high-density genetic map containing 11,488 single nucleotide polymorphisms (SNPs) and spanning 4202.12 cM in length. Transgressive segregation patterns and complex correlations in the five tested traits were observed. A total of 108 QTLs were found, including 13 major effect QTLs that contributed more than 10% toward phenotypic variation (PV) and 9 stable QTLs that could be repeatedly mapped in different generations. Chromosome A7 contained 12 QTL, ranking the first. No QTL was found on chromosomes D1 and D11. Two QTLs could be repeatedly detected in three populations, including qFL-D3-2 in F2, F2:4, and F2:5 with 9.18–21.45% of PV and qFS-A11-1 in F2:3, F2:4, and F2:5 with 6.05–10.41% of PV. Another seven stable QTLs could be detected in two populations, including four major effect QTLs: qFL-A12-3, qFS-D10-2, qMC-D6-2, and qMC-D8-1. Fourteen QTL-overlapping regions were found, which might explain the complex correlations among the five phenotypic traits. Four regions on chromosome A11, D3, D6, and D10 covered by both stable and major effect QTLs are promising for further fine mapping. The genomic regions of the two QTLs detected in three populations and the four major effect QTLs contain 810 genes. Gene functional analysis revealed that the annotated genes are mainly involved in protein binding and metabolic pathways. Fifteen candidate genes in the qFL-D3-2 region are highly expressed in fiber or ovules during fiber initiation, elongation, secondary cell wall thickening, or maturation stages. qRT-PCR revealed that Ghir_D03G005440.1 and Ghir_D03G011310.1 may play a role in promoting fiber initiation, while Ghir_D03G006470.1 may be beneficial for promoting fiber elongation. This study provides more information for revealing the molecular genetic basis underlying cotton fiber quality. [ABSTRACT FROM AUTHOR]

With the rapid emergence and distribution of red crown rot (RCR) across countries, durable sources of resistance against Calonectria ilicicola in soybean [Glycine max (L.) Merrill] is required to control the disease. We employed two RIL populations for the experiment. We identified 15 and 14 QTLs associated with RCR resistance in ZM6 and MN populations, respectively, totaling 29 QTLs. Six and eight QTLs had phenotypic variation above 10% in ZM6 and MN populations, respectively. We identified six (6) "QTL hotspots" for resistance to RCR from the ZM6 and MN RIL populations on chromosomes 1, 7, 10, 11, 13, and 18. Gene annotations, gene ontology enhancement, and RNA sequencing assessment detected 23 genes located within six "QTL Hotspots" as potential candidate genes that could govern RCR resistance in soybeans. Our data will generally assist breeders in rapidly and effectively incorporating RCR resistance into high-yielding accession through marker-assisted selection. [ABSTRACT FROM AUTHOR]

A well‐developed root system is essential for efficient nutrient and water uptake. We phenotyped a set of 172 Triticum durum–Aegilops speltoides backcross introgression lines (BILs) for various root architecture traits during 2019–2020 and 2020–2021 cropping seasons. The roots were sampled at the maximum tillering stage, and data on various root architecture traits were recorded. The quantitative trait loci (QTL) mapping was carried out using 5672 polymorphic SNPs obtained from genotyping‐by‐sequencing. A total of 21 QTLs were detected for various root architecture traits on chromosomes 1A, 2A, 2B, 3B, 5A and 6B. Stable QTLs were detected for total root length, number of root tips and root dry weight over the two seasons. Candidate genes were identified by scanning the physical interval corresponding to the linkage disequilibrium (LD) decay flanking the SNPs linked to the stable QTLs. In silico expression studies of postulated candidate genes revealed root‐specific upregulation of some of the genes. These QTLs can be used in breeding programmes after the development and validation of suitable marker assays. [ABSTRACT FROM AUTHOR]

Understanding the genetic basis of salt resistance in crops is crucial for agricultural productivity. This study investigates the phenotypic and genetic basis of salt stress response in rice (Oryza sativa L.), focusing on germination and seedling traits. Under salt stress conditions, significant differences were observed in seed germination and seedling traits between parental LH99 (Indica rice LuHui 99) and SN265 (japonica rice ShenNong 265). Transgressive segregation was evident within the RIL population, indicating complex genetic interactions. Nine QTLs were detected at germination and seedling stages under salt stress, namely qSGE5 and qSGE7 for seed germination energy (SGE); qSGP7 for seed germination percentage (SGP); qSSH7, qSSH9-1, and qSSH9-2 for seeding height (SSH); qSRN6 for root number (SRN); and qSDW6 and qSDW9 for dry weight (SDW). Among them, qSSH9-1 and qSDW9 were localized in the same interval, derived from the salt-resistant parent SN265. PCA revealed distinct trait patterns under salt stress, captured by six PCs explaining 81.12% of the total variance. PC composite scores were used to localize a QTL associated with early salt resistance in rice qESC9, which was located in the same interval as qSSH9-1 and qSDW9, and was subsequently unified under the name qESC9, an important QTL for early-growth salt tolerance in rice. Correlation analysis also confirmed a relationship between alleles of qESC9 and the resistance to salt, underscoring the critical role this locus plays in the determination of overall salt tolerance in rice. Physiological analyses of extreme phenotype lines highlighted the importance of ion exclusion mechanisms in salt-resistant lines, while salt-susceptible lines exhibited elevated oxidative stress and impaired antioxidant defense, contributing to cellular damage. This comprehensive analysis sheds light on the genetic and physiological mechanisms underlying salt stress response in rice, providing valuable insights for breeding programs aimed at enhancing salt resistance in rice. [ABSTRACT FROM AUTHOR]

Fruit weight is an important agronomic trait in pepper production and is closely related to yield. At present, many quantitative trait loci (QTL) related to fruit weight have been found in pepper; however, the genes affecting fruit weight remain unknown. We analyzed the fruit weight-related quantitative traits in an intraspecific Capsicum annuum cross between the cultivated species blocky-type pepper, cv. Qiemen, and the bird pepper accession, "129−1" (Capsicum annuum var. glatriusculum), which was the wild progenitor of C. annuum. Using the QTL-seq combined with the linkage-based QTL mapping approach, QTL detection was performed; and two major effects of QTL related to fruit weight, qFW2.1 and qFW3.1, were identified on chromosomes 2 and 3. The qFW2.1 maximum explained 12.28% of the phenotypic variance observed in two F2 generations, with the maximum LOD value of 11.02, respectively; meanwhile, the qFW3.1 maximum explained 15.50% of the observed phenotypic variance in the two F2 generations, with the maximum LOD value of 11.36, respectively. qFW2.1 was narrowed down to the 1.22 Mb region using homozygous recombinant screening from BC2S2 and BC2S3 populations, while qFW3.1 was narrowed down to the 4.61Mb region. According to the transcriptome results, a total of 47 and 86 differentially expressed genes (DEGs) in the candidate regions of qFW2.1 and qFW3.1 were identified. Further, 19 genes were selected for a qRT-PCR analysis based on sequence difference combined with the gene annotation. Finally, Capana02g002938 and Capana02g003021 are the most likely candidate genes for qFW2.1, and Capana03g000903 may be a candidate gene for qFW3.1. Taken together, our results identified and fine-mapped two major QTL for fruit weight in pepper that will facilitate marker-assistant breeding for the manipulation of yield in pepper. [ABSTRACT FROM AUTHOR]

Rice sheath blight is one of the most important fungal disease‐causing yield losses up to 50%. An Oryza rufipogon‐derived introgression line (Pusa 1908‐13‐12‐5) identified to be highly resistant to sheath blight was used for developing a RIL population by crossing with a highly susceptible rice cultivar, Pusa Basmati 1 (PB 1). The RIL population was genotyped with 80K Rice Pangenome (RPAN) single nucleotide polymorphism (SNP) array and phenotyped for disease response under artificial inoculation for 2 consecutive years. Inclusive composite interval mapping could identify six quantitative trait loci (QTLs) for two traits, namely, relative lesion height and relative yield loss per plant. Among these QTLs, four were major QTLs and three are novel QTLs. Three major QTLs were co‐localised within 1.4 Mb region on chromosome 1. In silico analysis revealed the presence of 12 candidate genes with potential role in disease resistance. Kompetitive Allele Specific PCR (KASP™) assay was developed for the linked SNPs and used for validation in an independent BC1F2:3 population (PB 1121/Pusa 1908‐13‐12‐5). One SNP (AX‐182186537) on chromosome 1 was validated, which offers scope for its utilisation in marker‐assisted breeding. [ABSTRACT FROM AUTHOR]

Detection of beneficial genes from wild accessions of cultivated crops is becoming increasingly important for crop improvement, especially for traits lost during domestication. A set of wild introgression lines derived from advanced back cross breeding of Swarna with Oryza nivara species were characterized for grain size and seedling vigor related traits. Grain length in the population varied between 7.23 and 8.22 mm, while width varied from 2.66 to 3.13 mm. The length-to-width ratio (LWR) ranged from 2.41 to 3.06 mm, showing various grain shapes in the population. Simultaneously, seedling vigor-related traits were studied, and a significant correlation was observed between seedling vigor traits and grain size parameters. Further mapping of quantitative trait loci (QTL) using simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) genotyping identified 18 QTL for seedling vigor- and grain size-related traits. Among these QTL, three major QTL (qAS7.1, qPL7.1 and qL7.1) were detected for grain size-related traits on chromosome 7, explaining 21.44%, 19.11% and 22.60% of phenotypic variation, respectively. Similarly, for seedling vigor traits, seven major QTL, viz., qSDW3.1, qTDW3.1, qSVI2-3.1, qSL3.1, qTL3.1, qSVI1-6.1, and qRDW8.1, were detected, explaining 18.3–26.38% of phenotypic variation. These QTL were on chromosomes 6 and 7 for seedling vigor and grain size traits and were collocated with common flanking markers. Hence, the results are useful for marker assisted breeding programmes for introgression and simultaneous improvement of seedling vigor and grain size, and further fine mapping of the related genes. [ABSTRACT FROM AUTHOR]

Improving low nitrogen (LN) tolerance in barley (Hordeum vulgare L.) increases global barley yield and quality. In this study, a recombinant inbred line (RIL) population crossed between "Baudin × CN4079" was used to conduct field experiments on twenty traits of barley yield, agronomy, and nitrogen(N)-related traits under LN and normal nitrogen (NN) treatments for two years. This study identified seventeen QTL, comprising eight QTL expressed under both LN and NN treatments, eight LN-specific QTL, and one NN-specific QTL. The localized C2 cluster contained QTL controlling yield, agronomic, and N-related traits. Of the four novel QTL, the expression of the N-related QTL Qstna.sau-5H and Qnhi.sau-5H was unaffected by N treatment. Qtgw.sau-2H for thousand-grain weight, Qph.sau-3H for plant height, Qsl.sau-7H for spike length, and Qal.sau-7H for awn length were identified to be the four stable expression QTL. Correlation studies revealed a significant negative correlation between grain N content and harvest index (p < 0.01). These results are essential for barley marker-assisted selection (MAS) breeding. [ABSTRACT FROM AUTHOR]

Background: Rapeseed (Brassica napus L.) is one of the most important oil crops and a wildly cultivated horticultural crop. The petals of B. napus serve to protect the reproductive organs and attract pollinators and tourists. Understanding the genetic basis of petal morphology regulation is necessary for B. napus breeding. Results: In the present study, the quantitative trait locus (QTL) analysis for six B. napus petal morphology parameters in a double haploid (DH) population was conducted across six microenvironments. A total of 243 QTLs and five QTL hotspots were observed, including 232 novel QTLs and three novel QTL hotspots. The spatiotemporal transcriptomic analysis of the diversiform petals was also conducted, which indicated that the expression of plant hormone metabolic and cytoskeletal binding protein genes was variant among diversiform petals. Conclusions: The integration of QTL and RNA-seq analysis revealed that plant hormones (including cytokinin, auxin, and gibberellin) and cytoskeleton were key regulators of the petal morphology. Subsequently, 61 high-confidence candidate genes of petal morphology regulation were identified, including Bn.SAUR10, Bn.ARF18, Bn.KIR1, Bn.NGA2, Bn.PRF1, and Bn.VLN4. The current study provided novel QTLs and candidate genes for further breeding B. napus varieties with diversiform petals. [ABSTRACT FROM AUTHOR]

Key message: QTL mapping combined with genome-wide association studies, revealed a potential candidate gene for resistance to northern leaf blight in the tropical CATETO-related maize line YML226, providing a basis for marker-assisted selection of maize varieties Northern leaf blight (NLB) is a foliar disease that can cause severe yield losses in maize. Identifying and utilizing NLB-resistant genes is the most effective way to prevent and control this disease. In this study, five important inbred lines of maize were used as parental lines to construct a multi-parent population for the identification of NLB-resistant loci. QTL mapping and GWAS analysis revealed that QTL qtl_YML226_1, which had the largest phenotypic variance explanation (PVE) of 9.28%, and SNP 5-49,193,921 were co-located in the CATETO-related line YML226. This locus was associated with the candidate gene Zm00001d014471, which encodes a pentatricopeptide repeat (PPR) protein. In the coding region of Zm00001d014471, YML226 had more specific SNPs than the other parental lines. qRT-PCR showed that the relative expressions of Zm00001d014471 in inoculated and uninoculated leaves of YML226 were significantly higher, indicating that the expression of the candidate gene was correlated with NLB resistance. The analysis showed that the higher expression level in YML226 might be caused by SNP mutations. This study identified NLB resistance candidate loci and genes in the tropical maize inbred line YML226 derived from the CATETO germplasm, thereby providing a theoretical basis for using modern marker-assisted breeding techniques to select genetic resources resistant to NLB. [ABSTRACT FROM AUTHOR]

Bakanae disease is mainly caused by Fusarium fujikuroi and is a significant fungal disease with a number of disastrous consequences. It causes great losses in rice production. However, few studies have focused on the details of bakanae disease resistance in rice. Here, we summarize and discuss the progress of bakanae disease resistance in rice. Besides rice germplasm screening and resistance-related gene/quantitative trait locus (QTL) exploration, the route of pathogen invasion in rice plants was determined. We further discussed the regulation of phytohormone-related genes and changes in endogenous phytohormones in rice plants that are induced by the pathogen. To achieve better control of bakanae disease, the use of natural fungicides was assessed in this review. During rice—F. fujikuroi interactions, the infection processes and spatial distribution of F. fujikuroi in infected seedlings and adult plants exhibit different trends. Fungal growth normally occurs both in resistant and susceptible cultivars, with less abundance in the former. Generally, bakanae disease is seed-borne, and seed disinfection using effective fungicides should always be the first and main option to better control the disease. Besides the friendly and effective measure of using natural fungicides, breeding and utilization of resistant rice cultivars is also an effective control method. To some extent, rice cultivars with low grain quality, indica subspecies, and some dwarf or semi-dwarf rice germplasms are more resistant to bakanae disease. Although no highly resistant germplasms were obtained, 37 QTLs were located, with almost half of the QTLs being located on chromosome 1. Using omics methods, WRKYs and MAPKs were usually found to be regulated during rice—F. fujikuroi interactions. The regulation of certain phytohormone-related genes and changes in some endogenous phytohormones induced by the pathogen were clear, i.e., it downregulated gibberellin-related genes and repressed endogenous gibberellins in resistant genotypes, but the opposite results were noted in susceptible rice genotypes. Overall, exploring resistant germplasms or resistance-related genes/QTLs for the breeding of rice with bakanae disease resistance, expanding research on the complex mechanism of rice—F. fujikuroi interactions, and using cost-effective and eco-friendly innovative control methods against the disease are necessary for present and future bakanae disease management. [ABSTRACT FROM AUTHOR]

Peanut stem rot, also known as white mold, poses a significant threat to peanut production. It is typically managed using fungicides and moderately resistant cultivars. Cultivars with higher resistance can reduce fungicide dependency and increase sustainability. This study explores the potential of wild peanut species in stem rot resistance breeding programs by enhancing genetic diversity in cultivated peanut. Through greenhouse and field evaluations, 13 allotetraploid hybrids with Arachis stenosperma as one of the parents showed superior resistance compared to other wild genotypes. The genomic regions that confer the stem rot resistance were further identified by genotyping and phenotyping an F2 population derived from the allotetraploid ValSten1 (A. valida × A. stenosperma)4× and A. hypogaea cv. TifGP-2. A linkage map was constructed from 1926 SNP markers. QTL analysis revealed both beneficial and deleterious loci, with two resistance-associated QTLs derived from A. stenosperma and four susceptibility loci, two from A. stenosperma and two from A. valida. This is the first study that evaluated peanut-compatible wild-derived allotetraploids for stem rot resistance and that identified wild-derived QTLs for resistance to this pathogen. The allotetraploid hybrid ValSten1, that has A. stenosperma as one of the parents, offers a resource for resistance breeding. Markers associated with resistance QTLs can facilitate introgression from ValSten1 into cultivated peanut varieties in future breeding efforts, potentially reducing reliance on chemical control measures. [ABSTRACT FROM AUTHOR]

In this study, a genetic linkage map was developed based on simple sequence repeat (SSR) markers to aid in the identification and expression analysis of gene loci underlying the quantitative trait loci (QTL) of starch content (SC) in cassava (Manihot esculenta). A total of 912 polymorphic loci from 4,515 tested SSRs were mapped into 18 linkage groups. QTL analysis revealed four loci with highly significant associations with starch. Gene annotation was performed, and potential genes related to starch synthesis were identified. Of these, expression of four genes related to starch synthesis (Raffinose synthase [RS], Phosphoenolpyruvate kinase [PK], Glucose-6-phosphate [G6P], and Glycogen synthase kinase 3 [GSK-3]) was investigated by real-time PCR assays. The results found a statistically significant difference (p < 0.05) at 3 months after planting (MAP) in all the tested genes, whereas a higher expression was detected in the low-SC group with specific genotypes of linked markers. A higher level of expression was observed in the RS, PK, and G6P genes at six and nine MAP, indicating that starch accumulation mainly occurs after 3 MAP, during which the root system begins to form. The potential genes identified in this study could provide a better understanding of the starch biosynthesis mechanism, and could be useful for applications in marker-assisted selection to facilitate cassava breeding programs in the future. [ABSTRACT FROM AUTHOR]

The watermelon (Citrullus lanatus L.) holds substantial economic value as a globally cultivated horticultural crop. However, the genetic architecture of watermelon fruit weight (FW) remains poorly understood. In this study, we used sh14-11 with small fruit and N14 with big fruit to construct 100 recombinant inbred lines (RILs). Based on whole-genome resequencing (WGR), 218,127 single nucleotide polymorphisms (SNPs) were detected to construct a high-quality genetic map. After quantitative trait loci (QTL) mapping, a candidate interval of 31–38 Mb on chromosome 2 was identified for FW. Simultaneously, the bulked segregant analysis (BSA) in the F2 population corroborated the identification of the same interval, encompassing the homologous gene linked to the known FW-related gene fas. Additionally, RNA-seq was carried out across 11 tissues from sh14-11 and N14, revealing expression profiles that identified 1695 new genes and corrected the annotation of 2941 genes. Subsequent differential expression analysis unveiled 8969 differentially expressed genes (DEGs), with 354 of these genes exhibiting significant differences across four key developmental stages. The integration of QTL mapping and differential expression analysis facilitated the identification of 14 FW-related genes, including annotated TGA and NAC transcription factors implicated in fruit development. This combined approach offers valuable insights into the genetic basis of FW, providing crucial resources for enhancing watermelon cultivation. [ABSTRACT FROM AUTHOR]