Population structure, genetic diversity and genomic selection signatures among a Brazilian common bean germplasm

Thermal treatment under oxidative conditions increases the antioxidant and antiglycation activity of Chilean Tórtola beans (Phaseolus vulgaris)

The influence of oxygen on the thermal treatment (TT) of secondary metabolite-enriched extracts (SMEEs) from Tórtola beans and procyanidin C1 (PC1) on the inhibition of advanced glycation end products (AGEs) generation in proteins was investigated. SMEE was incubated at 4 °C (control) or thermally treated at 60 °C for 2 h, at either 0 % O2 (I) or 20 % O2 (II). Treatments I and II increased the content of procyanidin dimers B2. Treatment II was more effective than the control or treatment I in preventing homocysteine oxidation and AGEs generation. TT of PC1 at 0 % or 20 % O2 generated procyanidin dimers and tetramers. PC1 TT at 20 % O2 exhibited higher oxidation potentials and lower IC50 values of fluorescent AGEs than those of controls or TT at 0 % O2. These findings indicate that SMEE from Tórtola beans after treatment II changes the degree of polymerization and oxidation procyanidins, thereby increasing their antiglycation activity.

Identifying the physiological traits associated with DNA marker using genome wide association in wheat under heat stress

Heat stress poses a significant environmental challenge that profoundly impacts wheat productivity. It disrupts vital physiological processes such as photosynthesis, by impeding the functionality of the photosynthetic apparatus and compromising plasma membrane stability, thereby detrimentally affecting grain development in wheat. The scarcity of identified marker trait associations pertinent to thermotolerance presents a formidable obstacle in the development of marker-assisted selection strategies against heat stress. To address this, wheat accessions were systematically exposed to both normal and heat stress conditions and phenotypic data were collected on physiological traits including proline content, canopy temperature depression, cell membrane injury, photosynthetic rate, transpiration rate (at vegetative and reproductive stage and 'stay-green'. Principal component analysis elucidated the most significant contributors being proline content, transpiration rate, and canopy temperature depression, which exhibited a synergistic relationship with grain yield. Remarkably, cluster analysis delineated the wheat accessions into four discrete groups based on physiological attributes. Moreover, to explore the relationship between physiological traits and DNA markers, 158 wheat accessions were genotyped with 186 SSRs. Allelic frequency and polymorphic information content value were found to be highest on genome A (4.94 and 0.688), chromosome 1A (5.00 and 0.712), and marker Xgwm44 (13.0 and 0.916). Population structure, principal coordinate analysis and cluster analysis also partitioned the wheat accessions into four subpopulations based on genotypic data, highlighting their genetic homogeneity. Population diversity and presence of linkage disequilibrium established the suitability of population for association mapping. Additionally, linkage disequilibrium decay was most pronounced within a 15-20 cM region on chromosome 1A. Association mapping revealed highly significant marker trait associations at Bonferroni correction P < 0.00027. Markers Xwmc418 (located on chromosome 3D) and Xgwm233 (chromosome 7A) demonstrated associations with transpiration rate, while marker Xgwm494 (chromosome 3A) exhibited an association with photosynthetic rates at both vegetative and reproductive stages under heat stress conditions. Additionally, markers Xwmc201 (chromosome 6A) and Xcfa2129 (chromosome 1A) displayed robust associations with canopy temperature depression, while markers Xbarc163 (chromosome 4B) and Xbarc49 (chromosome 5A) were strongly associated with cell membrane injury at both stages. Notably, marker Xbarc49 (chromosome 5A) exhibited a significant association with the 'stay-green' trait under heat stress conditions. These results offers the potential utility in marker-assisted selection, gene pyramiding and genomic selection models to predict performance of wheat accession under heat stress conditions.

Screening of Triploid Banana Population Under Natural and Controlled Black Sigatoka Disease for Genomic Selection

Black sigatoka disease (BSD) is the most important foliar threat in banana production, and breeding efforts against it should take advantage of genomic selection (GS), which has become one of the most explored tools to increase genetic gain, save time, and reduce selection costs. To evaluate the potential of GS in banana for BSD, 210 triploid accessions were obtained from the African Banana and Plantain Research Center to constitute a training population. The variability in the population was assessed at the phenotypic level using BSD- and agronomic-related traits and at the molecular level using single-nucleotide polymorphisms (SNPs). The analysis of variance showed a significant difference between accessions for almost all traits measured, although at the genomic group level, there was no significant difference for BSD-related traits. The index of non-spotted leaves among accessions ranged from 0.11 to 0.8. The accessions screening in controlled conditions confirmed the susceptibility of all genomic groups to BSD. The principal components analysis with phenotypic data revealed no clear diversity partition of the population. However, the structure analysis and the hierarchical clustering analysis with SNPs grouped the population into four clusters and two subpopulations, respectively. The field and laboratory screening of the banana GS training population confirmed that all genomic groups are susceptible to BSD but did not reveal any genetic structure, whereas SNP markers exhibited clear genetic structure and provided useful information in the perspective of applying GS.

Analysis of population structure and genetic diversity of Camellia tachangensis in Guizhou based on SNP markers

BACKGROUND

Camellia tachangensis F. C. Zhang is a five-compartment species in the ovary of tea group plants, which represents the original germline of early differentiation of some tea group plants.

METHODS AND RESULTS

In this study, we analyzed single-nucleotide polymorphisms (SNPs) at the genome level, constructed a phylogenetic tree, analyzed the genetic diversity, and further investigated the population structure of 100 C. tachangensis accessions using the genotyping-by-sequencing (GBS) method. A total of 91,959 high-quality SNPs were obtained. Population structure analysis showed that the 100 C. tachangensis accessions clustered into three groups: YQ-1 (Village Group), YQ-2 (Forest Group) and YQ-3 (Transition Group), which was further consistent with the results of phylogenetic analysis and principal component analyses (PCA). In addition, a comparative analysis of the genetic diversity among the three populations (Forest, Village, and Transition Groups) detected the highest genetic diversity in the Transition Group and the highest differentiation between Forest and Village Groups.

CONCLUSIONS

C. tachangensis plants growing in the forest had different genetic backgrounds from those growing in villages. This study provides a basis for the effective protection and utilization of C. tachangensis populations and lays a foundation for future C. tachangensis breeding.

A genomic toolkit for winged bean Psophocarpus tetragonolobus

A sustainable supply of plant protein is critical for future generations and needs to be achieved while reducing green house gas emissions from agriculture and increasing agricultural resilience in the face of climate volatility. Agricultural diversification with more nutrient-rich and stress tolerant crops could provide the solution. However, this is often hampered by the limited availability of genomic resources and the lack of understanding of the genetic structure of breeding germplasm and the inheritance of important traits. One such crop with potential is winged bean (Psophocarpus tetragonolobus), a high seed protein tropical legume which has been termed 'the soybean for the tropics'. Here, we present a chromosome level winged bean genome assembly, an investigation of the genetic diversity of 130 worldwide accessions, together with two linked genetic maps and a trait QTL analysis (and expression studies) for regions of the genome with desirable ideotype traits for breeding, namely architecture, protein content and phytonutrients.

Phaseolus vulgaris mutants reveal variation in the nuclear genome

Phaseolus vulgaris L. (common bean) is an essential source of proteins in the human diet worldwide. Bean breeding programs to increase genetic diversity based on induced mutagenesis have a long tradition in Bulgaria. Common bean varieties with high productivity, wide environmental adaptability, good nutritional properties, and improved disease resistance have been successfully developed. In this study, we aimed to investigate selected nuclear genome features, such as the genome size, the number and chromosomal distribution of 5S and 35S rDNA loci by using the fluorescence in situ hybridization (FISH), as well as the level of DNA damage in some local Bulgarian accessions and mutants of P. vulgaris. Flow cytometry analyses revealed no significant differences in genome size between analyzed lines except for one of the analyzed mutants, M19. The value of genome size 2C DNA is about 1.37 pg2C -1 for all lines, whereas it is 1.42 pg2C-1 for M19. The chromosome number remains the same (2n=22) for all analyzed lines. Results of FISH analyses showed that the number of 5S rDNA was stable among accessions and mutant lines (four loci), while the number of 35S rDNA loci was shown as highly polymorphic, varying between ten and sixteen, and displaying differences in the size and location of 35S rDNA loci between analyzed genotypes. The cell cycle profile was different for the analyzed genotypes. The results revealed that wide variation in genome organization and size as well as DNA damage characterizes the analyzed genetic resources of the common bean.

Mapping yield and yield-related traits using diverse common bean germplasm

Common bean (bean) is one of the most important legume crops, and mapping genes for yield and yield-related traits is essential for its improvement. However, yield is a complex trait that is typically controlled by many loci in crop genomes. The objective of this research was to identify regions in the bean genome associated with yield and a number of yield-related traits using a collection of 121 diverse bean genotypes with different yields. The beans were evaluated in replicated trials at two locations, over two years. Significant variation among genotypes was identified for all traits analyzed in the four environments. The collection was genotyped with the BARCBean6K_3 chip (5,398 SNPs), two yield/antiyield gene-based markers, and seven markers previously associated with resistance to common bacterial blight (CBB), including a Niemann-Pick polymorphism (NPP) gene-based marker. Over 90% of the single-nucleotide polymorphisms (SNPs) were polymorphic and separated the panel into two main groups of small-seeded and large-seeded beans, reflecting their Mesoamerican and Andean origins. Thirty-nine significant marker-trait associations (MTAs) were identified between 31 SNPs and 15 analyzed traits on all 11 bean chromosomes. Some of these MTAs confirmed genome regions previously associated with the yield and yield-related traits in bean, but a number of associations were not reported previously, especially those with derived traits. Over 600 candidate genes with different functional annotations were identified for the analyzed traits in the 200-Kb region centered on significant SNPs. Fourteen SNPs were identified within the gene model sequences, and five additional SNPs significantly associated with five different traits were located at less than 0.6 Kb from the candidate genes. The work confirmed associations between two yield/antiyield gene-based markers (AYD1m and AYD2m) on chromosome Pv09 with yield and identified their association with a number of yield-related traits, including seed weight. The results also confirmed the usefulness of the NPP marker in screening for CBB resistance. Since disease resistance and yield measurements are environmentally dependent and labor-intensive, the three gene-based markers (CBB- and two yield-related) and quantitative trait loci (QTL) that were validated in this work may be useful tools for simplifying and accelerating the selection of high-yielding and CBB-resistant bean cultivars.

Narrow genetic diversity in germplasm from the Guinean and Sudano-Guinean zones in Benin indicates the need to broaden the genetic base of sweet fig banana (Musa acuminata cv Sotoumon)

Sweet fig (M. acuminata cv. Sotoumon) is an economically important dessert banana in Benin, with high nutritional, medicinal, and cultural values. Nevertheless, its productivity and yield are threatened by biotic and abiotic stresses. Relevant knowledge of the genetic diversity of this economically important crop is essential for germplasm conservation and the development of breeding programs. However, very little is known about the genetic makeup of this cultivar in Benin. To advance the understanding of genetic diversity in sweet fig banana germplasm, a Genotype-By-Sequencing (GBS) was performed on a panel of 273 accessions collected in different phytogeographical zones of Benin. GBS generated 8,457 quality SNPs, of which 1992 were used for analysis after filtering. The results revealed a low diversity in the studied germplasm (He = 0.0162). Genetic differentiation was overall very low in the collection as suggested by the negative differentiation index (Fstg = -0.003). The Analysis of Molecular Variance (AMOVA) indicated that the variation between accessions within populations accounted for 83.8% of the total variation observed (P < 0.001). The analysis of population structure and neighbor-joining tree partitioned the germplasm into three clusters out of which a predominant major one contained 98.1% of all accessions. These findings demonstrate that current sweet fig banana genotypes shared a common genetic background, which made them vulnerable to biotic and abiotic stress. Therefore, broadening the genetic base of the crop while maintaining its quality attributes and improving yield performance is of paramount importance. Moreover, the large genetic group constitutes an asset for future genomic selection studies in the crop and can guide the profiling of its conservation strategies.

Genetic Parameter and Hyper-Parameter Estimation Underlie Nitrogen Use Efficiency in Bread Wheat

Estimation and prediction play a key role in breeding programs. Currently, phenotyping of complex traits such as nitrogen use efficiency (NUE) in wheat is still expensive, requires high-throughput technologies and is very time consuming compared to genotyping. Therefore, researchers are trying to predict phenotypes based on marker information. Genetic parameters such as population structure, genomic relationship matrix, marker density and sample size are major factors that increase the performance and accuracy of a model. However, they play an important role in adjusting the statistically significant false discovery rate (FDR) threshold in estimation. In parallel, there are many genetic hyper-parameters that are hidden and not represented in the given genomic selection (GS) model but have significant effects on the results, such as panel size, number of markers, minor allele frequency, number of call rates for each marker, number of cross validations and batch size in the training set of the genomic file. The main challenge is to ensure the reliability and accuracy of predicted breeding values (BVs) as results. Our study has confirmed the results of bias-variance tradeoff and adaptive prediction error for the ensemble-learning-based model STACK, which has the highest performance when estimating genetic parameters and hyper-parameters in a given GS model compared to other models.

Whole-genome resequencing of common bean elite breeding lines

The expansion of bean genome technologies has prompted new perspectives on generating resources and knowledge essential to research and implementing biotechnological tools for the practical operations of plant breeding programs. This study aimed to resequence the entire genome (whole genome sequencing-WGS) of 40 bean genotypes selected based on their significance in breeding programs worldwide, with the objective of generating an extensive database for the identification of single nucleotide polymorphisms (SNPs). Over 6 million SNPs were identified, distributed across the 11 bean chromosomes. After quality variant filtering, 420,509 high-quality SNPs were established, with an average of 38,228 SNPs per chromosome. These variants were categorized based on their predicted effects, revealing that the majority exerted a modifier impact on non-coding genome regions (94.68%). Notably, a significant proportion of SNPs occurred in intergenic regions (62.89%) and at least one SNP was identified in 58.63% of the genes annotated in the bean genome. Of particular interest, 7841 SNPs were identified in 85% of the putative plant disease defense-related genes, presenting a valuable resource for crop breeding efforts. These findings provide a foundation for the development of innovative and broadly applicable technologies for the routine selection of superior genotypes in global bean improvement and germplasm characterization programs.

Genome-wide association analysis reveals the optimal genomic regions for pod size in bean

The snap bean is the most commonly grown vegetable legume worldwide, and its pod size is both an important yield and appearance quality trait. However, the improvement of pod size in snap beans grown in China has been largely hindered by a lack of information on the specific genes that determine pod size. In this study, we identified 88 snap bean accessions and evaluated their pod size traits. Through a genome-wide association study (GWAS), 57 single nucleotide polymorphisms (SNPs) significantly associated with pod size were detected. Candidate gene analysis showed that cytochrome P450 family genes, WRKY, and MYB transcription factors were the predominant candidate genes for pod development, and eight of these 26 candidate genes showed relatively higher expression patterns in flowers and young pods. A significant pod length (PL) SNP and a single pod weight (SPW) SNP were successfully converted into kompetitive allele-specific polymerase chain reaction (KASP) markers and validated in the panel. These results enhance our understanding of the genetic basis of pod size, and also provide genetic resources for the molecular breeding of pod size in snap beans.

Assessing the Genetic Diversity of Daylily Germplasm Using SSR Markers: Implications for Daylily Breeding

This work aims to characterize the genetic diversity of species, early hybrids, and cultivars using microsatellite simple sequence repeat (SSR) markers, as well as analyze and identify the origin of Hemerocallis spp. early hybrids. For this research, samples were collected from different types of daylily species, early hybrids (known or hypothetically first-generation hybrids from Hemerocallis species), foreign, and Lithuanian varieties. An initial screening of SSR primers developed for Hemerocallis citrina was performed, and their suitability for testing other daylily species and hybrids was evaluated. The genetic diversity was assessed with the selected eight-primer set, and molecular SSR profiles were created. Primer SAU00097 is the most informative according to heterozygosity (0.95) and polymorphism information content (PIC) (0.17). The highest heterozygosity was observed in Lithuanian cultivars (0.713), the lowest in species (0.583). Genetic relationships between species show that only fulvous daylilies are separated into a different cluster. The highest variation among genotypes was observed in the species group (18%), while modern cultivars had the slightest variation among genotypes (1%). The putative origin of early hybrids was analyzed using a likelihood heatmap of all genotypes. Results show what species might be used in breeding for early hybrids. Several modern diploid and tetraploid daylily cultivars have triploid species as ancestors.

Utilizing Genomics to Characterize the Common Oat Gene Pool—The Story of More than a Century of Polish Breeding

This study was undertaken to investigate the diversity and population structure of 487 oat accessions, including breeding lines from the ongoing programs of the three largest Polish breeding companies, along with modern and historical Polish and foreign cultivars. The analysis was based on 7411 DArTseq-derived SNPs distributed among three sub-genomes (A, C, and D). The heterogeneity of the studied material was very low, as only cultivars and advanced breeding lines were examined. Principal component analysis (PCA), principal coordinate analysis (PCoA), and cluster and STRUCTURE analyses found congruent results, which show that most of the examined cultivars and materials from Polish breeding programs formed major gene pools, that only some accessions derived from Strzelce Plant Breeding, and that foreign cultivars were outside of the main group. During the 120 year oat breeding process, only 67 alleles from the old gene pool were lost and replaced by 67 new alleles. The obtained results indicate that no erosion of genetic diversity was observed within the Polish native oat gene pool. Moreover, current oat breeding programs have introduced 673 new alleles into the gene pool relative to historical cultivars. The analysis also showed that most of the changes in relation to historical cultivars occurred within the A sub-genome with emphasis on chromosome 6A. The targeted changes were the rarest in the C sub-genome. This study showed that Polish oat breeding based mainly on traditional breeding methods—although focused on improving traits typical to this crop, i.e., enhancing the grain yield and quality and improving adaptability—did not significantly narrow the oat gene pool and in fact produced cultivars that are not only competitive in the European market but are also reservoirs of new alleles that were not found in the analyzed foreign materials.

Genome-wide association mapping for LLS resistance in a MAGIC population of groundnut (Arachis hypogaea L.)

The identified 30 functional nucleotide polymorphisms or genic SNP markers would offer essential information for marker-assisted breeding in groundnut. A genome-wide association study (GWAS) on component traits of LLS resistance in an eight-way multiparent advance generation intercross (MAGIC) population of groundnut in the field and in a light chamber (controlled conditions) was performed via an Affymetrix 48 K single-nucleotide polymorphism (SNP) 'Axiom Arachis' array. Multiparental populations with high-density genotyping enable the detection of novel alleles. In total, five quantitative trait loci (QTLs) with marker - log10(p value) scores ranging from 4.25 to 13.77 for the incubation period (IP) and six QTLs with marker - log10(p value) scores ranging from 4.33 to 10.79 for the latent period (LP) were identified across the A- and B-subgenomes. A total of 62 markers‒trait associations (MTAs) were identified across the A- and B-subgenomes. Markers for LLS scores and the area under the disease progression curve (AUDPC) recorded for plants in the light chamber and under field conditions presented - log10 (p value) scores ranging from 4.22 to 27.30. The highest number of MTAs (six) was identified on chromosomes A05, B07 and B09. Out of a total of 73 MTAs, 37 and 36 MTAs were detected in subgenomes A and B, respectively. Taken together, these results suggest that both subgenomes have equal potential genomic regions contributing to LLS resistance. A total of 30 functional nucleotide polymorphisms or genic SNP markers were detected, among which eight genes were found to encode leucine-rich repeat (LRR) receptor-like protein kinases and putative disease resistance proteins. These important SNPs can be used in breeding programmes for the development of cultivars with improved disease resistance.

Agro-morphological and genetic variability analysis in oat germplasms with special emphasis on food and feed

The gaining attention of underutilized oat crops for both food and feed, mining of quality and yield related genes/QTLs from available germplasms of oat is need of the hour. The large family of grasses has a vast number of germplasms that could be harnessed for bio-prospecting. The selection of cross-compatible oat germplasms by molecular markers could be used for the introgression of the novel traits into the elite background of oats. The process needs a thorough study of genetic diversity to see the evolutionary relatedness among germplasms. Considering this, in the present study, the genetic diversity of 38 oat germplasms with 12 agro-morphological traits was carried out using 22 Inter Simple Sequence Repeat (ISSR) markers. We found a high level of polymorphism and 158 distinctive alleles; on average 7.18 alleles per primer, further, high-yielding genotypes were identified with the help of phenotypic data and genetic diversity was analyzed by using DNA fingerprint-based principal component analysis, UPGMA dendrogram. Among these 38 germplasms; eight were identified as superior under high grain yield (OS-424, OS-403, NDO-1101, OL-10, UPO-212, OS-405, OS-6, and OS-346) and another eight germplasms were identified as superior for the high fresh weight (for fodder purpose, NDO-711, RO-19, OL-14, OL-1760/OL-11, NDO-10, UPO-212, UPO-06-1, and RO-11-1). These results suggest that germplasms that are closely related (Cross-compatible) and have good potential for desirable traits could be used for varietal development by using marker-assisted selection.

Multi-locus genome-wide association studies reveal genomic regions and putative candidate genes associated with leaf spot diseases in African groundnut (Arachis hypogaea L.) germplasm

Early leaf spot (ELS) and late leaf spot (LLS) diseases are the two most destructive groundnut diseases in Ghana resulting in ≤ 70% yield losses which is controlled largely by chemical method. To develop leaf spot resistant varieties, the present study was undertaken to identify single nucleotide polymorphism (SNP) markers and putative candidate genes underlying both ELS and LLS. In this study, six multi-locus models of genome-wide association study were conducted with the best linear unbiased predictor obtained from 294 African groundnut germplasm screened for ELS and LLS as well as image-based indices of leaf spot diseases severity in 2020 and 2021 and 8,772 high-quality SNPs from a 48 K SNP array Axiom platform. Ninety-seven SNPs associated with ELS, LLS and five image-based indices across the chromosomes in the 2 two sub-genomes. From these, twenty-nine unique SNPs were detected by at least two models for one or more traits across 16 chromosomes with explained phenotypic variation ranging from 0.01 - 62.76%, with exception of chromosome (Chr) 08 (Chr08), Chr10, Chr11, and Chr19. Seventeen potential candidate genes were predicted at ± 300 kbp of the stable/prominent SNP positions (12 and 5, down- and upstream, respectively). The results from this study provide a basis for understanding the genetic architecture of ELS and LLS diseases in African groundnut germplasm, and the associated SNPs and predicted candidate genes would be valuable for breeding leaf spot diseases resistant varieties upon further validation.

Novel candidate loci for morpho-agronomic and seed quality traits detected by targeted genotyping-by-sequencing in common bean

Phaseolus vulgaris L., known as common bean, is one of the most important grain legumes cultivated around the world for its immature pods and dry seeds, which are rich in protein and micronutrients. Common bean offers a cheap food and protein sources to ameliorate food shortage and malnutrition around the world. However, the genetic basis of most important traits in common bean remains unknown. This study aimed at identifying QTL and candidate gene models underlying twenty-six agronomically important traits in common bean. For this, we assembled and phenotyped a diversity panel of 200 P. vulgaris genotypes in the greenhouse, comprising determinate bushy, determinate climbing and indeterminate climbing beans. The panel included dry beans and snap beans from different breeding programmes, elite lines and landraces from around the world with a major focus on accessions of African, European and South American origin. The panel was genotyped using a cost-conscious targeted genotyping-by-sequencing (GBS) platform to take advantage of highly polymorphic SNPs detected in previous studies and in diverse germplasm. The detected single nucleotide polymorphisms (SNPs) were applied in marker-trait analysis and revealed sixty-two quantitative trait loci (QTL) significantly associated with sixteen traits. Gene model identification via a similarity-based approach implicated major candidate gene models underlying the QTL associated with ten traits including, flowering, yield, seed quality, pod and seed characteristics. Our study revealed six QTL for pod shattering including three new QTL potentially useful for breeding. However, the panel was evaluated in a single greenhouse environment and the findings should be corroborated by evaluations across different field environments. Some of the detected QTL and a number of candidate gene models only elucidate the understanding of the genetic nature of these traits and provide the basis for further studies. Finally, the study showed the possibility of using a limited number of SNPs in performing marker-trait association in common bean by applying a highly scalable targeted GBS approach. This targeted GBS approach is a cost-efficient strategy for assessment of the genetic basis of complex traits and can enable geneticists and breeders to identify novel loci and targets for marker-assisted breeding more efficiently.

Determining Genetic Diversity and Population Structure of Common Bean (Phaseolus vulgaris L.) Landraces from Türkiye Using SSR Markers

Assessment of genetic diversity among different varieties helps to improve desired characteristics of crops, including disease resistance, early maturity, high yield, and resistance to drought. Molecular markers are one of the most effective tools for discovering genetic diversity that can increase reproductive efficiency. Simple sequence repeats (SSRs), which are codominant markers, are preferred for the determination of genetic diversity because they are highly polymorphic, multi-allelic, highly reproducible, and have good genome coverage. This study aimed to determine the genetic diversity of 40 common bean (Phaseolus vulgaris L.) landraces collected from the Ispir district located in the Northeast Anatolia region of Türkiye and five commercial varieties using SSR markers. The Twenty-seven SSR markers produced a total of 142 polymorphic bands, ranging from 2 (GATS91 and PVTT001) to 12 (BM153) alleles per marker, with an average number of 5.26 alleles. The gene diversity per marker varied between 0.37 and 0.87 for BM053 and BM153 markers, respectively. When heterozygous individuals are calculated proportional to the population, the heterozygosity ranged from 0.00 to 1.00, with an average of 0.30. The expected heterozygosity of the SSR locus ranged from 0.37 (BM053) to 0.88 (BM153), with an average of 0.69. Nei's gene diversity scored an average of 0.69. The polymorphic information content (PIC) values of SSR markers varied from 0.33 (BM053) to 0.86 (BM153), with an average of 0.63 per locus. The greatest genetic distance (0.83) was between lines 49, 50, 53, and cultivar Karacaşehir-90, while the shortest (0.08) was between lines 6 and 26. In cluster analysis using Nei's genetic distance, 45 common bean genotypes were divided into three groups and very little relationship was found between the genotypes and the geographical distances. In genetic structure analysis, three subgroups were formed, including local landraces and commercial varieties. The result confirmed that the rich diversity existing in Ispir bean landraces could be used as a genetic resource in designing breeding programs and may also contribute to Türkiye bean breeding programs.

Quantitative Trait Locus Mapping of Marsh Spot Disease Resistance in Cranberry Common Bean (Phaseolus vulgaris L.)

Common bean (Phaseolus vulgaris L.) is a food crop that is an important source of dietary proteins and carbohydrates. Marsh spot is a physiological disorder that diminishes seed quality in beans. Prior research suggested that this disease is likely caused by manganese (Mn) deficiency during seed development and that marsh spot resistance is controlled by at least four genes. In this study, genetic mapping was performed to identify quantitative trait loci (QTL) and the potential candidate genes associated with marsh spot resistance. All 138 recombinant inbred lines (RILs) from a bi-parental population were evaluated for marsh spot resistance during five years from 2015 to 2019 in sandy and heavy clay soils in Morden, Manitoba, Canada. The RILs were sequenced using a genotyping by sequencing approach. A total of 52,676 single nucleotide polymorphisms (SNPs) were identified and filtered to generate a high-quality set of 2066 SNPs for QTL mapping. A genetic map based on 1273 SNP markers distributed on 11 chromosomes and covering 1599 cm was constructed. A total of 12 stable and 4 environment-specific QTL were identified using additive effect models, and an additional two epistatic QTL interacting with two of the 16 QTL were identified using an epistasis model. Genome-wide scans of the candidate genes identified 13 metal transport-related candidate genes co-locating within six QTL regions. In particular, two QTL (QTL.3.1 and QTL.3.2) with the highest R2 values (21.8% and 24.5%, respectively) harbored several metal transport genes Phvul.003G086300, Phvul.003G092500, Phvul.003G104900, Phvul.003G099700, and Phvul.003G108900 in a large genomic region of 16.8–27.5 Mb on chromosome 3. These results advance the current understanding of the genetic mechanisms of marsh spot resistance in cranberry common bean and provide new genomic resources for use in genomics-assisted breeding and for candidate gene isolation and functional characterization.

Identification and characterization of chickpea genotypes for early flowering and higher seed germination through molecular markers

BACKGROUND

Chickpea is the fourth most important legume crop contributing 15.42% to the total legume production and a rich source of proteins, minerals, and vitamins. Determination of genetic diversity of wild and elite cultivars coupled with early flowering and higher seed germination lines are quintessential for variety improvement.

METHODS AND RESULTS

In the present study, we have analyzed the genetic diversity, population structure, cross-species transferability, and allelic richness in 50 chickpea collections using 23 Inter simple sequence repeats (ISSR) markers. The observed parameters such as allele number varied from 3 to 16, range of allele size varied from 150 to 1600 bp and polymorphic information content (PIC) range lies in between 0.15 and 0.49. Dendrogram was constructed with ISSR marker genotypic data and classified 50 chickpea germplasms into groups I and II, where the accession P 74 - 1 is in group I and the rest are in group II. Dendrogram, Principal component analysis (PCA), dissimilarity matrix, and Bayesian model-based genetic clustering of 50 chickpea germplasms revealed that P 74 - 1 and P 1883 are very diverse chickpea accessions.

CONCLUSION

Based on genetic diversity analysis, 15 chickpea germplasm having been screened for early flowering and higher seed germination and found that the P 1857-1 and P 3971 have early flowering and higher seed germination percentage in comparison to P 1883 and other germplasm. These agronomic traits are essential for crop improvement and imply the potential of ISSR markers in crop improvement.

Genome-Wide Association Study and Genomic Prediction for Bacterial Wilt Resistance in Common Bean (Phaseolus vulgaris) Core Collection

Common bean (Phaseolus vulgaris) is one of the major legume crops cultivated worldwide. Bacterial wilt (BW) of common bean (Curtobacterium flaccumfaciens pv. flaccumfaciens), being a seed-borne disease, has been a challenge in common bean producing regions. A genome-wide association study (GWAS) was conducted to identify SNP markers associated with BW resistance in the USDA common bean core collection. A total of 168 accessions were evaluated for resistance against three different isolates of BW. Our study identified a total of 14 single nucleotide polymorphism (SNP) markers associated with the resistance to BW isolates 528, 557, and 597 using mixed linear models (MLMs) in BLINK, FarmCPU, GAPIT, and TASSEL 5. These SNPs were located on chromosomes Phaseolus vulgaris [Pv]02, Pv04, Pv08, and Pv09 for isolate 528; Pv07, Pv10, and Pv11 for isolate 557; and Pv04, Pv08, and Pv10 for isolate 597. The genomic prediction accuracy was assessed by utilizing seven GP models with 1) all the 4,568 SNPs and 2) the 14 SNP markers. The overall prediction accuracy (PA) ranged from 0.30 to 0.56 for resistance against the three BW isolates. A total of 14 candidate genes were discovered for BW resistance located on chromosomes Pv02, Pv04, Pv07, Pv08, and Pv09. This study revealed vital information for developing genetic resistance against the BW pathogen in common bean. Accordingly, the identified SNP markers and candidate genes can be utilized in common bean molecular breeding programs to develop novel resistant cultivars.

Morphological and molecular characterization of variation in common bean (Phaseolus vulgaris L.) germplasm from Azad Jammu and Kashmir, Pakistan

Phaseolus vulgaris, an essential food and source of protein, is cultivated across the world. This study was carried out to investigate the diversity and population structure of 34 P. vulgaris landrace accessions collected from the Azad Jammu and Kashmir (AJ&K) regions of Pakistan. The samples were analyzed both morphologically and using genetic variation identified through RNA sequencing. Our results indicated that most genetic variation occurs among local accessions, with little genetic variation occurring between geographical regions. In addition, the accessions fell into two major genetic groups. Morphological analysis revealed that these two genetic groups differ in a number of quantitative traits, including seed length, seed width, and seed weight. One accession, DUD-11, appears to be a mixture of the two major groups genetically as well as morphologically. Among the other accessions, DUD-8, RWK-2, and NGD-1 depicted particularly high seed weight along with higher seed length, seed width, and seed yield per plant. We suggest focusing on these accessions in future breeding programs. More generally, our results provide baseline data that will be useful for crop improvement and effective cultivation practices in Pakistan.

Tracking Changes in the Spring Barley Gene Pool in Poland during 120 Years of Breeding

This study was undertaken to investigate the diversity and population structure of 83 spring barley (Hordeum vulgare L.) cultivars, which corresponded to 120 years of this crop's breeding in Poland. The analysis was based on 11,655 DArTseq-derived SNPs evenly distributed across seven barley chromosomes. Five groups were assigned in the studied cultivars according to the period of their breeding. A decrease in observed heterozygosity within the groups was noted along with the progress in breeding, with a simultaneous increase in the inbreeding coefficient value. As a result of breeding, some of the unique allelic variation present in old cultivars was lost, but crosses with foreign materials also provided new alleles to the barley gene pool. It is important to mention that the above changes affected different chromosomes to varying degrees. The internal variability of the cultivars ranged from 0.011 to 0.236. Internal uniformity was lowest among the oldest cultivars, although some highly homogeneous ones were found among them. This is probably an effect of genetic drift or selection during their multiplications and regenerations in the period from breeding to the time of analysis. The population genetic structure of the studied group of cultivars appears to be quite complex. It was shown that their genetic makeup consists of as many as eleven distinct gene pools. The analysis also showed traces of directed selection on chromosomes 3H and 5H. Detailed data analysis confirmed the presence of duplicates for 11 cultivars. The performed research will allow both improvement of the management of barley genetic resources in the gene bank and the reuse of this rich and forgotten variability in breeding programs and research.

Genome-wide association studies dissect the genetic architecture of seed shape and size in common bean

Seed weight and size are important yield components. Thus, selecting for large seeds has been a key objective in crop domestication and breeding. In common bean, seed shape is also important since it influences industrial processing and plays a vital role in determining the choices of consumers and farmers. In this study, we performed genome-wide association studies on a core collection of common bean accessions to dissect the genetic architecture and identify genomic regions associated with seed morphological traits related to weight, size, and shape. Phenotypic data were collected by high-throughput image-based approaches, and utilized to test associations with 10,362 single-nucleotide polymorphism markers using multilocus mixed models. We searched within genome-associated regions for candidate genes putatively involved in seed phenotypic variation. The collection exhibited high variability for the entire set of seed traits, and the Andean gene pool was found to produce larger, heavier seeds than the Mesoamerican gene pool. Strong pairwise correlations were verified for most seed traits. Genome-wide association studies identified marker-trait associations accounting for a considerable amount of phenotypic variation in length, width, projected area, perimeter, and circularity in 4 distinct genomic regions. Promising candidate genes were identified, e.g. those encoding an AT-hook motif nuclear-localized protein 8, type 2C protein phosphatases, and a protein Mei2-like 4 isoform, known to be associated with seed size and weight regulation. Moreover, the genes that were pinpointed are also good candidates for functional analysis to validate their influence on seed shape and size in common bean and other related crops.

Unravelling the Genetic Architecture of Rust Resistance in the Common Bean (Phaseolus vulgaris L.) by Combining QTL-Seq and GWAS Analysis

The common bean (Phaseolus vulgaris L.) is the most important legume crop directly used for human consumption worldwide. Bean rust, caused by Uromyces appendiculatus, is a devastating disease and usually causes severe loss of seed yield and pod quality. Deployment of resistant cultivars is the best strategy to combat this disease. However, despite being the largest snap bean-producing country, the genetic basis research of rust resistance has largely lagged in China. In this study, an RIL population and a diversity panel were evaluated for rust resistance against a purified rust isolate Cua-LS using a detached leaf assay. Deploying a QTL-Seq analysis in the RIL population, a 1.81 Mb interval on chromosome 4, a 2.73 Mb interval on chromosome 5 and a 1.26 Mb interval on chromosome 6 were identified as major QTLs for rust resistance, designated as Qur-1, Qur-2 and Qur-3, respectively. Through a GWAS diversity panel, 64 significant SNPs associated with rust resistance were detected, distributed in all 11 chromosomes and explaining 19–49% of the phenotypic variation. Synteny analysis showed that Qur-2 was validated in GWAS, but the rust QTL/SNPs detected in our study were different from the known genes, except Ur-11. A total of 114 candidate genes, including the typical NBS-LRR genes, protein kinase superfamily proteins and ABC transporter family proteins, were identified and proposed as the likely candidates. The identified 17 resistant accessions will enrich the resistant germplasm resources, and the detected QTLs/SNPs will facilitate the molecular breeding of rust resistance in the common bean.

Population structure analysis to explore genetic diversity and geographical distribution characteristics of cultivated-type tea plant in Guizhou Plateau

BACKGROUND

Tea plants originated in southwestern China. Guizhou Plateau is an original center of tea plants, and is rich in germplasm resources. However, the genetic diversity, population structure and distribution characteristics of cultivated-type tea plants in the region are unknown. In this study, we explored the genetic diversity and geographical distribution of cultivated-type tea accessions in Guizhou Plateau.

RESULTS

We used 112,072 high-quality genotyping-by-sequencing to analyze the genetic diversity, principal components, phylogeny, population structure, and linkage disequilibrium, and develop a core collection of 253 cultivated-type tea plant accessions from Guizhou Plateau. The results showed Genetic diversity of the cultivated-type tea accessions of the Pearl River Basin was significantly higher than that of the cultivated-type tea accessions of the Yangtze River Basin. Three inferred pure groups (CG-1, CG-2 and CG-3) and one inferred admixture group (CG-4), were identified by a population structure analysis, and verified by principal component and phylogenetic analyses. The highest genetic distance and differentiation coefficients were determined for CG-2 vs CG-3. The lower genetic distance and differentiation coefficients were determined for CG-4 vs CG-2 and CG-4 vs CG-3, respectively. We developed a core set and a primary set. The primary and core sets contained 77.0 and 33.6% of all individuals in the initial set, respectively. The primary set may serve as the primary population in genome-wide association studies, while the core collection may serve as the core population in multiple treatment setting studies.

CONCLUSIONS

The present study demonstrated the genetic diversity and geographical distribution characteristics of cultivated-type tea plants in Guizhou Plateau. Significant differences in genetic diversity and evolutionary direction were detected between the ancient landraces of the Pearl River Basin and the those of the Yangtze River Basin. Major rivers and ancient hubs were largely responsible for the genetic exchange between the Pearl River Basin and the Yangtze River Basin ancient landraces as well as the formation of the ancient hubs evolutionary group. Genetic diversity, population structure and core collection elucidated by this study will facilitate further genetic studies, germplasm protection, and breeding of tea plants.

Genetic diversity of Norway spruce ecotypes assessed by GBS-derived SNPs

We investigated the genetic structure of three phenotypically distinct ecotypic groups of Norway spruce (Picea abies) belonging to three elevational classes; namely, low- (acuminata), medium- (europaea), and high-elevation (obovata) form, each represented by 150 trees. After rigorous filtering, we used 1916 Genotyping-by-Sequencing generated SNPs for analysis. Outputs from three multivariate analysis methods (Bayesian clustering algorithm implemented in STRUCTURE, Principal Component Analysis, and the Discriminant Analysis of Principal Components) indicated the presence of a distinct genetic cluster representing the high-elevation ecotypic group. Our findings bring a vital message to forestry practice affirming that artificial transfer of forest reproductive material, especially for stands under harsh climate conditions, should be considered with caution.

Multivariate genomic analysis and optimal contributions selection predicts high genetic gains in cooking time, iron, zinc, and grain yield in common beans in East Africa

Common bean (Phaseolus vulgaris L.) is important in African diets for protein, iron (Fe), and zinc (Zn), but traditional cultivars have long cooking time (CKT), which increases the time, energy, and health costs of cooking. Genomic selection was used to predict genomic estimated breeding values (GEBV) for grain yield (GY), CKT, Fe, and Zn in an African bean panel of 358 genotypes in a two-stage analysis. In Stage 1, best linear unbiased estimates (BLUE) for each trait were obtained from 898 genotypes across 33 field trials in East Africa. In Stage 2, BLUE in a training population of 141 genotypes were used in a multivariate genomic analysis with genome-wide single nucleotide polymorphism data from the African bean panel. Moderate to high genomic heritability was found for GY (0.45 ± 0.10), CKT (0.50 ± 0.15), Fe (0.57 ± 0.12), and Zn (0.61 ± 0.13). There were significant favorable genetic correlations between Fe and Zn (0.91 ± 0.06), GY and Fe (0.66 ± 0.17), GY and Zn (0.44 ± 0.19), CKT and Fe (-0.57 ± 0.21), and CKT and Zn (-0.67 ± 0.20). Optimal contributions selection (OCS), based on economic index of weighted GEBV for each trait, was used to design crossing within four market groups relevant to East Africa. Progeny were predicted by OCS to increase in mean GY by 12.4%, decrease in mean CKT by 9.3%, and increase in mean Fe and Zn content by 6.9 and 4.6%, respectively, with low achieved coancestry of 0.032. Genomic selection with OCS will accelerate breeding of high-yielding, biofortified, and rapid cooking African common bean cultivars.

Genome-Wide Association Study Identifies Genomic Regions for Important Morpho-Agronomic Traits in Mesoamerican Common Bean

The population growth trend in recent decades has resulted in continuing efforts to guarantee food security in which leguminous plants, such as the common bean (Phaseolus vulgaris L.), play a particularly important role as they are relatively cheap and have high nutritional value. To meet this demand for food, the main target for genetic improvement programs is to increase productivity, which is a complex quantitative trait influenced by many component traits. This research aims to identify Quantitative Trait Nucleotides (QTNs) associated with productivity and its components using multi-locus genome-wide association studies. Ten morpho-agronomic traits [plant height (PH), first pod insertion height (FPIH), number of nodules (NN), pod length (PL), total number of pods per plant (NPP), number of locules per pod (LP), number of seeds per pod (SP), total seed weight per plant (TSW), 100-seed weight (W100), and grain yield (YLD)] were evaluated in four environments for 178 Mesoamerican common bean domesticated accessions belonging to the Brazilian Diversity Panel. In order to identify stable QTNs, only those identified by multiple methods (mrMLM, FASTmrMLM, pLARmEB, and ISIS EM-BLASSO) or in multiple environments were selected. Among the identified QTNs, 64 were detected at least thrice by different methods or in different environments, and 39 showed significant phenotypic differences between their corresponding alleles. The alleles that positively increased the corresponding traits, except PH (for which lower values are desired), were considered favorable alleles. The most influenced trait by the accumulation of favorable alleles was PH, showing a 51.7% reduction, while NN, TSW, YLD, FPIH, and NPP increased between 18 and 34%. Identifying QTNs in several environments (four environments and overall adjusted mean) and by multiple methods reinforces the reliability of the associations obtained and the importance of conducting these studies in multiple environments. Using these QTNs through molecular techniques for genetic improvement, such as marker-assisted selection or genomic selection, can be a strategy to increase common bean production.

Genome-wide association study for grain mineral content in a Brazilian common bean diversity panel

QTNs significantly associated to nine mineral content in grains of common bean were identified. The accumulation of favorable alleles was associated with a gradually increasing nutrient content in the grain. Biofortification is one of the strategies developed to address malnutrition in developing countries, the aim of which is to improve the nutritional content of crops. The common bean (Phaseolus vulgaris L.), a staple food in several African and Latin American countries, has excellent nutritional attributes and is considered a strong candidate for biofortification. The objective of this study was to identify genomic regions associated with nutritional content in common bean grains using 178 Mesoamerican accessions belonging to a Brazilian Diversity Panel (BDP) and 25,011 good-quality single nucleotide polymorphisms. The BDP was phenotyped in three environments for nine nutrients (phosphorus, potassium, calcium, magnesium, copper, manganese, sulfur, zinc, and iron) using four genome-wide association multi-locus methods. To obtain more accurate results, only quantitative trait nucleotides (QTNs) that showed repeatability (i.e., those detected at least twice using different methods or environments) were considered. Forty-eight QTNs detected for the nine minerals showed repeatability and were considered reliable. Pleiotropic QTNs and overlapping genomic regions surrounding the QTNs were identified, demonstrating the possible association between the deposition mechanisms of different nutrients in grains. The accumulation of favorable alleles in the same accession was associated with a gradually increasing nutrient content in the grain. The BDP proved to be a valuable source for association studies. The investigation of different methods and environments showed the reliability of markers associated with minerals. The loci identified in this study will potentially contribute to the improvement of Mesoamerican common beans, particularly carioca and black beans, the main groups consumed in Brazil.

Genetic diversity and inter-gene pool introgression of Mesoamerican Diversity Panel in common beans

Brazil is among the largest producers and consumers of common bean (Phaseolus vulgaris L.) and can be considered a secondary center of diversity for the species. The aim of this study was to estimate the genetic diversity, population structure, and relationships among 288 common bean accessions in an American Diversity Panel (ADP) genotyped with 4,042 high-quality single nucleotide polymorphisms (SNPs). The results showed inter-gene pool hybridization (hybrids) between the two main gene pools (i.e., Mesoamerican and Andean), based on principal component analysis (PCA), discriminant analysis of principal components (DAPC), and STRUCTURE analysis. The genetic diversity parameters showed that the Mesoamerican group has higher values of diversity and allelic richness in comparison with the Andean group. Considering the optimal clusters (K), clustering was performed according to the type of grain (i.e., market group), the institution of origin, the period of release, and agronomic traits. A new subset was selected and named the Mesoamerican Diversity Panel (MDP), with 205 Mesoamerican accessions. Analysis of molecular variance (AMOVA) showed low genetic variance between the two panels (i.e., ADP and MDP) with the highest percentage of the limited variance among accessions in each group. The ADP showed occurrence of high genetic differentiation between populations (i.e., Mesoamerican and Andean) and introgression between gene pools in hybrids based on a set of diagnostic SNPs. The MDP showed better linkage disequilibrium (LD) decay. The availability of genetic variation from inter-gene pool hybridizations presents a potential opportunity for breeders towards the development of superior common bean cultivars.

Genome-wide association analysis of bean fly resistance and agro-morphological traits in common bean

The bean fly (Ophiomyia spp) is a key insect pest causing significant crop damage and yield loss in common bean (Phaseolus vulgaris L., 2n = 2x = 22). Development and deployment of agronomic superior and bean fly resistant common bean varieties aredependent on genetic variation and the identification of genes and genomic regions controlling economic traits. This study's objective was to determine the population structure of a diverse panel of common bean genotypes and deduce associations between bean fly resistance and agronomic traits based on single nucleotide polymorphism (SNP) markers. Ninety-nine common bean genotypes were phenotyped in two seasons at two locations and genotyped with 16 565 SNP markers. The genotypes exhibited significant variation for bean fly damage severity (BDS), plant mortality rate (PMR), and pupa count (PC). Likewise, the genotypes showed significant variation for agro-morphological traits such as days to flowering (DTF), days to maturity (DTM), number of pods per plant (NPP), number of seeds per pod (NSP), and grain yield (GYD). The genotypes were delineated into two populations, which were based on the Andean and Mesoamerican gene pools. The genotypes exhibited a minimum membership coefficient of 0.60 to their respective populations. Eighty-three significant (P<0.01) markers were identified with an average linkage disequilibrium of 0.20 at 12Mb across the 11 chromosomes. Three markers were identified, each having pleiotropic effects on two traits: M100049197 (BDS and NPP), M3379537 (DTF and PC), and M13122571 (NPP and GYD). The identified markers are useful for marker-assisted selection in the breeding program to develop common bean genotypes with resistance to bean fly damage.

Morpho-agronomic, biochemical and molecular analysis of genetic diversity in the Mesoamerican common bean panel

The common bean (Phaseolus vulgaris L.) is of great importance to the food and nutritional security of many populations, and exploitation of the crop's genetic diversity is essential for the success of breeding programs. Thus, the aim of the present study was to evaluate the genetic diversity of 215 common bean accessions, which included cultivars, obsolete cultivars, improved lines, and landraces using morpho-agronomic and biochemical traits, and amplified fragment length polymorphism markers (AFLP). Genetic parameters, box plots, Pearson's correlation analysis, and Ward's hierarchical clustering were used to analyze the data. The Jaccard similarity coefficient and neighbour-joining clustering method were used for molecular analysis. A wide variability among the accessions was observed for morpho-agronomic and biochemical traits. Selective accuracy (Ac) and broad-sense heritability (h2) values were high to intermediate for all traits, except seed yield. Ward's hierarchical clustering analysis generated six groups. AFLP analysis also revealed significant differences among the accessions. There was no correlation between the differences based on genetic markers and those based on morpho-agronomic and biochemical data, which indicates that both datasets are important for elucidating the differences among accessions. The results of the present study indicate great genetic diversity among the evaluated accessions.