Major Contribution of Flowering Time and Vegetative Growth to Plant Production in Common Bean As Deduced from a Comparative Genetic Mapping

GWAS of resistance to three bacterial diseases in the Andean common bean diversity panel

Bacterial brown spot (BBS) caused by Pseudomonas syringae pv. syringae (Pss), common bacterial blight (CBB) caused by Xanthomonas axonopodis pv. phaseoli (Xap) and Xanthomonas fuscans subsp. fuscans (Xff), and halo bacterial blight (HBB), caused by Pseudomonas syringae pv. phaseolicola (Psph), are major bacterial diseases that severely affect common bean yields and global food security. Andean-origin dry beans, representing large-seeded market classes, are particularly susceptible. Using 140,325 SNPs, a multi-locus GWAS was conducted on subsets of the Andean diversity panel (ADP) phenotyped for BBS in South Africa, CBB in Puerto Rico, South Africa, and Zambia, and HBB in South Africa, through natural infection, artificial inoculation, or both. Twenty-four QTL associated with resistance were identified: nine for BBS, eight for CBB, and seven for HBB. Four QTL intervals on Pv01, Pv03, Pv05, and Pv08 overlapped with BBS and HBB resistance. A genomic interval on Pv01, near the fin gene, which determines growth habit, was linked to resistance to all three pathogens. Different QTLs were detected for BBS and CBB resistance when phenotyped under natural infection versus artificial inoculation. These results underscore the importance of combining phenotyping methods in multi-GWAS to capture the full genetic spectrum. Previously recognized CBB resistance QTL SAP6 and SU91 and HBB resistance QTL HB4.2, and HB5.1, were observed. Other common (MAF >0.25) and rare (MAF <0.05) resistance QTL were also detected. Overall, these findings enhance the understanding and utilization of bacterial resistance present in ADP for the development of common beans with improved resistance.

QTL mapping for pod quality and yield traits in snap bean (Phaseolus vulgaris L.)

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.

Phenotypic and genetic characterization of a near-isogenic line pair: insights into flowering time in chickpea

BACKGROUND

Cicer arietinum is a significant legume crop cultivated mainly in short-season environments, where early-flowering is a desirable trait to overcome terminal constraints. Despite its agricultural significance, the genetic control of flowering time in chickpea is not fully understood. In this study, we developed, phenotyped, re-sequenced and genetically characterized a pair of near-isogenic lines (NILs) with contrasting days to flowering to identify candidate gene variants potentially associated with flowering time.

RESULTS

In addition to days to flowering, noticeable differences in multiple shoot architecture traits were observed between the NILs. The resequencing data confirms that the NILs developed in this study serve as appropriate plant materials, effectively constraining genetic variation to specific regions and thereby establishing a valuable resource for future genetic and functional investigations in chickpea research. Leveraging bioinformatics tools and public genomic datasets, we identified homologs of flowering-related genes from Arabidopsis thaliana, including ELF3 and, for the first time in chickpea, MED16 and STO/BBX24, with variants among the NILs. Analysis of the allelic distribution of these genes revealed their preservation within chickpea diversity and their potential association with flowering time. Variants were also identified in members of the ERF and ARF gene families. Furthermore, in silico expression analysis was conducted elucidating their putative roles in flowering.

CONCLUSIONS

While the gene CaELF3a is identified as a prominent candidate, this study also exposes new targets in chickpea, such as CaMED16b and LOC101499101 (BBX24-like), homologs of flowering-related genes in Arabidopsis, as well as ERF12 and ARF2. The in silico expression characterization and genetic variability analysis performed could contribute to their use as specific markers for chickpea breeding programs. This study lays the groundwork for future investigations utilizing this plant material, promising further insights into the complex mechanisms governing flowering time in chickpea.

Identification of superior haplotypes for flowering time in pigeonpea through candidate gene-based association study of a diverse minicore collection

KEY MESSAGE

In current study candidate gene (261 genes) based association mapping on 144 pigeonpea accessions for flowering time and related traits and 29 MTAs producing eight superior haplotypes were identified. In the current study, we have conducted an association analysis for flowering-associated traits in a diverse pigeonpea mini-core collection comprising 144 accessions using the SNP data of 261 flowering-related genes. In total, 13,449 SNPs were detected in the current study, which ranged from 743 (ICP10228) to 1469 (ICP6668) among the individuals. The nucleotide diversity (0.28) and Watterson estimates (0.34) reflected substantial diversity, while Tajima's D (-0.70) indicated the abundance of rare alleles in the collection. A total of 29 marker trait associations (MTAs) were identified, among which 19 were unique to days to first flowering (DOF) and/or days to fifty percent flowering (DFF), 9 to plant height (PH), and 1 to determinate (Det) growth habit using 3 years of phenotypic data. Among these MTAs, six were common to DOF and/or DFF, and four were common to DOF/DFF along with the PH, reflecting their pleiotropic action. These 29 MTAs spanned 25 genes, among which 10 genes clustered in the protein-protein network analysis, indicating their concerted involvement in floral induction. Furthermore, we identified eight haplotypes, four of which regulate late flowering, while the remaining four regulate early flowering using the MTAs. Interestingly, haplotypes conferring late flowering (H001, H002, and H008) were found to be taller, while those involved in early flowering (H003) were shorter in height. The expression pattern of these genes, as inferred from the transcriptome data, also underpinned their involvement in floral induction. The haplotypes identified will be highly useful to the pigeonpea breeding community for haplotype-based breeding.

Identification of consistent QTL and candidate genes associated with seed traits in common bean by combining GWAS and RNA-Seq

KEY MESSAGE

Association analysis, colocation study with previously reported QTL, and differential expression analyses allowed the identification of the consistent QTLs and main candidate genes controlling seed traits. Common beans show wide seed variations in shape, size, water uptake, and coat proportion. This study aimed to identify consistent genomic regions and candidate genes involved in the genetic control of seed traits by combining association and differential expression analyses. In total, 298 lines from the Spanish Diversity Panel were genotyped with 4,658 SNP and phenotyped for seven seed traits in three seasons. Thirty-eight significant SNP-trait associations were detected, which were grouped into 23 QTL genomic regions with 1,605 predicted genes. The positions of the five QTL regions associated with seed weight were consistent with previously reported QTL. HCPC analysis using the SNP that tagged these five QTL regions revealed three main clusters with significantly different seed weights. This analysis also separated groups that corresponded well with the two gene pools described: Andean and Mesoamerican. Expression analysis was performed on the seeds of the cultivar 'Xana' in three seed development stages, and 1,992 differentially expressed genes (DEGs) were detected, mainly when comparing the early and late seed development stages (1,934 DEGs). Overall, 91 DEGs related to cell growth, signaling pathways, and transcriptomic factors underlying these 23 QTL were identified. Twenty-two DEGs were located in the five QTL regions associated with seed weight, suggesting that they are the main set of candidate genes controlling this character. The results confirmed that seed weight is the sum of the effects of a complex network of loci, and contributed to the understanding of seed phenotype control.

Transcriptome-wide association mapping provides insights into the genetic basis and candidate genes governing flowering, maturity and seed weight in rice bean (Vigna umbellata)

BACKGROUND

Rice bean (Vigna umbellata), an underrated legume, adapts to diverse climatic conditions with the potential to support food and nutritional security worldwide. It is used as a vegetable, minor food crop and a fodder crop, being a rich source of proteins, minerals, and essential fatty acids. However, little effort has been made to decipher the genetic and molecular basis of various useful traits in this crop. Therefore, we considered three economically important traits i.e., flowering, maturity and seed weight of rice bean and identified the associated candidate genes employing an associative transcriptomics approach on 100 diverse genotypes out of 1800 evaluated rice bean accessions from the Indian National Genebank.

RESULTS

The transcriptomics-based genotyping of one-hundred diverse rice bean cultivars followed by pre-processing of genotypic data resulted in 49,271 filtered markers. The STRUCTURE, PCA and Neighbor-Joining clustering of 100 genotypes revealed three putative sub-populations. The marker-trait association analysis involving various genome-wide association study (GWAS) models revealed significant association of 82 markers on 48 transcripts for flowering, 26 markers on 22 transcripts for maturity and 22 markers on 21 transcripts for seed weight. The transcript annotation provided information on the putative candidate genes for the considered traits. The candidate genes identified for flowering include HSC80, P-II PsbX, phospholipid-transporting-ATPase-9, pectin-acetylesterase-8 and E3-ubiquitin-protein-ligase-RHG1A. Further, the WRKY1 and DEAD-box-RH27 were found to be associated with seed weight. Furthermore, the associations of PIF3 and pentatricopeptide-repeat-containing-gene with maturity and seed weight, and aldo-keto-reductase with flowering and maturity were revealed.

CONCLUSION

This study offers insights into the genetic basis of key agronomic traits in rice bean, including flowering, maturity, and seed weight. The identified markers and associated candidate genes provide valuable resources for future exploration and targeted breeding, aiming to enhance the agronomic performance of rice bean cultivars. Notably, this research represents the first transcriptome-wide association study in pulse crop, uncovering the candidate genes for agronomically useful traits.

Genetic control of pod morphological traits and pod edibility in a common bean RIL population

KEY MESSAGE

QTL mapping, association analysis, and colocation study with previously reported QTL revealed three main regions controlling pod morphological traits and two loci for edible pod characteristics on the common bean chromosomes Pv01 and Pv06. Bean pod phenotype is a complex characteristic defined by the combination of different traits that determine the potential use of a genotype as a snap bean. In this study, the TUM RIL population derived from a cross between 'TU' (dry) and 'Musica' (snap) was used to investigate the genetic control of pod phenotype. The character was dissected into pod morphological traits (PMTs) and edible pod characteristics (EPC). The results revealed 35 QTL for PMTs located on seven chromosomes, suggesting a strong QTL colocation on chromosomes Pv01 and Pv06. Some QTL were colocated with previously reported QTL, leading to the mapping of 15 consensus regions associated with bean PMTs. Analysis of EPC of cooked beans revealed that two major loci with epistatic effect, located on chromosomes Pv01 and Pv06, are involved in the genetic control of this trait. An association study using a subset of the Spanish Diversity Panel (snap vs. non-snap) detected 23 genomic regions, with three regions being mapped at a position similar to those of two loci identified in the TUM population. The results demonstrated the relevant roles of Pv01 and Pv06 in the modulation of bean pod phenotype. Gene ontology enrichment analysis revealed a significant overrepresentation of genes regulating the phenylpropanoid metabolic process and auxin response in regions associated with PMTs and EPC, respectively. Both biological functions converged in the lignin biosynthetic pathway, suggesting the key role of the pathway in the genetic control of bean pod phenotype.

Genetic erosion within the Fabada dry bean market class revealed by high-throughput genotyping

The Fabada market class within the dry beans has a well-differentiated seed phenotype with very large white seeds. This work investigated the genetic diversity maintained in the seed collections within this market class and possible genetic erosion over the last 30 years. A panel with 100 accessions was maintained in seed collections for 30 years, 57 accessions collected from farmers in 2021, six cultivars developed in SERIDA, and 16 reference cultivars were gathered and genotyped with 108,585 SNPs using the genotyping-by-sequencing method. Filtering based on genotypic and phenotypic data was carried out in a staggered way to investigate the genetic diversity among populations. The dendrogram generated from genotyping revealed 90 lines forming 16 groups with identical SNP profiles (redundant lines) from 159 lines classified as market-class Fabada according to their passport data. Seed phenotyping indicated that 19 lines were mistakenly classified as Fabada (homonymies), which was confirmed in the dendrogram built without redundant lines. Moreover, this study provides evidence of genetic erosion between the population preserved for 30 years and the currently cultivated population. The conserved population contains 54.6% segregation sites and 41 different SNP profiles, whereas the cultivated population has 19.6% segregation sites and 26 SNP profiles. The loss of genetic variability cannot be attributed to the diffusion of modern cultivars, which increase genetic diversity (six new SNP profiles). The results allow for the more efficient preservation of plant genetic resources in genebanks, minimizing redundant accessions and incorporating new variations based on genotypic and phenotypic data.

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.

Genome-wide association study of 23 flowering phenology traits and 4 floral agronomic traits in tree peony (Paeonia section Moutan DC.) reveals five genes known to regulate flowering time

Tree peony is a unique traditional flower in China, with large, fragrant, and colorful flowers. However, a relatively short and concentrated flowering period limits the applications and production of tree peony. A genome-wide association study (GWAS) was conducted to accelerate molecular breeding for the improvement of flowering phenology traits and ornamental phenotypes in tree peony. A diverse panel of 451 tree peony accessions was phenotyped for 23 flowering phenology traits and 4 floral agronomic traits over 3 years. Genotyping by sequencing (GBS) was used to obtain a large number of genome-wide single-nucleotide polymorphisms (SNPs) (107 050) for the panel genotypes, and 1047 candidate genes were identified by association mapping. Eighty-two related genes were observed during at least 2 years for flowering, and seven SNPs repeatedly identified for multiple flowering phenology traits over multiple years were highly significantly associated with five genes known to regulate flowering time. We validated the temporal expression profiles of these candidate genes and highlighted their possible roles in the regulation of flower bud differentiation and flowering time in tree peony. This study shows that GWAS based on GBS can be used to identify the genetic determinants of complex traits in tree peony. The results expand our understanding of flowering time control in perennial woody plants. Identification of markers closely related to these flowering phenology traits can be used in tree peony breeding programs for important agronomic traits.

A genome wide association study to dissect the genetic architecture of agronomic traits in Andean lupin (Lupinus mutabilis)

Establishing Lupinus mutabilis as a protein and oil crop requires improved varieties adapted to EU climates. The genetic regulation of strategic breeding traits, including plant architecture, growing cycle length and yield, is unknown. This study aimed to identify associations between 16 669 single nucleotide polymorphisms (SNPs) and 9 agronomic traits on a panel of 223 L. mutabilis accessions, grown in four environments, by applying a genome wide association study (GWAS). Seven environment-specific QTLs linked to vegetative yield, plant height, pods number and flowering time, were identified as major effect QTLs, being able to capture 6 to 20% of the phenotypic variation observed in these traits. Furthermore, two QTLs across environments were identified for flowering time on chromosome 8. The genes FAF, GAMYB and LNK, regulating major pathways involved in flowering and growth habit, as well as GA30X1, BIM1, Dr1, HDA15, HAT3, interacting with these pathways in response to hormonal and environmental cues, were prosed as candidate genes. These results are pivotal to accelerate the development of L. mutabilis varieties adapted to European cropping conditions by using marker-assisted selection (MAS), as well as to provide a framework for further functional studies on plant development and phenology in this species.

Breeding of Vegetable Cowpea for Nutrition and Climate Resilience in Sub-Saharan Africa: Progress, Opportunities, and Challenges

Currently, the world population is increasing, and humanity is facing food and nutritional scarcity. Climate change and variability are a major threat to global food and nutritional security, reducing crop productivity in the tropical and subtropical regions of the globe. Cowpea has the potential to make a significant contribution to global food and nutritional security. In addition, it can be part of a sustainable food system, being a genetic resource for future crop improvement, contributing to resilience and improving agricultural sustainability under climate change conditions. In malnutrition prone regions of sub-Saharan Africa (SSA) countries, cowpea has become a strategic dryland legume crop for addressing food insecurity and malnutrition. Therefore, this review aims to assess the contribution of cowpea to SSA countries as a climate-resilient crop and the existing production challenges and perspectives. Cowpea leaves and immature pods are rich in diverse nutrients, with high levels of protein, vitamins, macro and micronutrients, minerals, fiber, and carbohydrates compared to its grain. In addition, cowpea is truly a multifunctional crop for maintaining good health and for reducing non-communicable human diseases. However, as a leafy vegetable, cowpea has not been researched and promoted sufficiently because it has not been promoted as a food security crop due to its low yield potential, susceptibility to biotic and abiotic stresses, quality assurance issues, policy regulation, and cultural beliefs (it is considered a livestock feed). The development of superior cowpea as a leafy vegetable can be approached in different ways, such as conventional breeding and gene stacking, speed breeding, mutation breeding, space breeding, demand-led breeding, a pan-omics approach, and local government policies. The successful breeding of cowpea genotypes that are high-yielding with a good nutritional value as well as having resistance to biotics and tolerant to abiotic stress could also be used to address food security and malnutrition-related challenges in sub-Saharan Africa.

Improving Association Studies and Genomic Predictions for Climbing Beans With Data From Bush Bean Populations

Common bean (Phaseolus vulgaris L.) has two major origins of domestication, Andean and Mesoamerican, which contribute to the high diversity of growth type, pod and seed characteristics. The climbing growth habit is associated with increased days to flowering (DF), seed iron concentration (SdFe), nitrogen fixation, and yield. However, breeding efforts in climbing beans have been limited and independent from bush type beans. To advance climbing bean breeding, we carried out genome-wide association studies and genomic predictions using 1,869 common bean lines belonging to five breeding panels representing both gene pools and all growth types. The phenotypic data were collected from 17 field trials and were complemented with 16 previously published trials. Overall, 38 significant marker-trait associations were identified for growth habit, 14 for DF, 13 for 100 seed weight, three for SdFe, and one for yield. Except for DF, the results suggest a common genetic basis for traits across all panels and growth types. Seven QTL associated with growth habits were confirmed from earlier studies and four plausible candidate genes for SdFe and 100 seed weight were newly identified. Furthermore, the genomic prediction accuracy for SdFe and yield in climbing beans improved up to 8.8% when bush-type bean lines were included in the training population. In conclusion, a large population from different gene pools and growth types across multiple breeding panels increased the power of genomic analyses and provides a solid and diverse germplasm base for genetic improvement of common bean.

Revisiting the Domestication Process of African Vigna Species (Fabaceae): Background, Perspectives and Challenges

Legumes are one of the most economically important and biodiverse families in plants recognised as the basis to develop functional foods. Among these, the Vigna genus stands out as a good representative because of its relatively recent African origin as well as its outstanding potential. Africa is a great biodiversity centre in which a great number of species are spread, but only three of them, Vigna unguiculata, Vigna subterranea and Vigna vexillata, were successfully domesticated. This review aims at analysing and valorising these species by considering the perspective of human activity and what effects it exerts. For each species, we revised the origin history and gave a focus on where, when and how many times domestication occurred. We provided a brief summary of bioactive compounds naturally occurring in these species that are fundamental for human wellbeing. The great number of wild lineages is a key point to improve landraces since the domestication process caused a loss of gene diversity. Their genomes hide a precious gene pool yet mostly unexplored, and genes lost during human activity can be recovered from the wild lineages and reintroduced in cultivated forms through modern technologies. Finally, we describe how all this information is game-changing to the design of future crops by domesticating de novo.

Genome-Wide Association Study Reveals Candidate Genes for Flowering Time in Cowpea (Vigna unguiculata [L.] Walp.)

Cowpea (Vigna unguiculata [L.] Walp., diploid, 2n = 22) is a major crop used as a protein source for human consumption as well as a quality feed for livestock. It is drought and heat tolerant and has been bred to develop varieties that are resilient to changing climates. Plant adaptation to new climates and their yield are strongly affected by flowering time. Therefore, understanding the genetic basis of flowering time is critical to advance cowpea breeding. The aim of this study was to perform genome-wide association studies (GWAS) to identify marker trait associations for flowering time in cowpea using single nucleotide polymorphism (SNP) markers. A total of 368 accessions from a cowpea mini-core collection were evaluated in Ft. Collins, CO in 2019 and 2020, and 292 accessions were evaluated in Citra, FL in 2018. These accessions were genotyped using the Cowpea iSelect Consortium Array that contained 51,128 SNPs. GWAS revealed seven reliable SNPs for flowering time that explained 8-12% of the phenotypic variance. Candidate genes including FT, GI, CRY2, LSH3, UGT87A2, LIF2, and HTA9 that are associated with flowering time were identified for the significant SNP markers. Further efforts to validate these loci will help to understand their role in flowering time in cowpea, and it could facilitate the transfer of some of this knowledge to other closely related legume species.

Physiological and genetic characterization of heat stress effects in a common bean RIL population

Heat stress is a major abiotic stress factor reducing crop productivity and climate change models predict increasing temperatures in many production regions. Common bean (Phaseolus vulgaris L.) is an important crop for food security in the tropics and heat stress is expected to cause increasing yield losses. To study physiological responses and to characterize the genetics of heat stress tolerance, we evaluated the recombinant inbred line (RIL) population IJR (Indeterminate Jamaica Red) x AFR298 of the Andean gene pool. Heat stress (HS) conditions in the field affected many traits across the reproductive phase. High nighttime temperatures appeared to have larger effects than maximum daytime temperatures. Yield was reduced compared to non-stress conditions by 37% and 26% in 2016 and 2017 seasons, respectively. The image analysis tool HYRBEAN was developed to evaluate pollen viability (PolVia). A significant reduction of PolVia was observed in HS and higher viability was correlated with yield only under stress conditions. In susceptible lines the reproductive phase was extended and defects in the initiation of seed, seed fill and seed formation were identified reducing grain quality. Higher yields under HS were correlated with early flowering, high pollen viability and effective seed filling. Quantitative trait loci (QTL) analysis revealed a QTL for both pod harvest index and PolVia on chromosome Pv05, for which the more heat tolerant parent IJR contributed the positive allele. Also, on chromosome Pv08 a QTL from IJR improved PolVia and the yield component pods per plant. HS affected several traits during the whole reproductive development, from floral induction to grain quality traits, indicating a general heat perception affecting many reproductive processes. Identification of tolerant germplasm, indicator traits for heat tolerance and molecular tools will help to breed heat tolerant varieties to face future climate change effects.

GWAS of pod morphological and color characters in common bean

BACKGROUND

Common bean (Phaseolus vulgaris L.) is an important legume species which can be consumed as immature pods and dry seeds after re-hydration and cooking. Many genes and QTL, and epistatic interactions among them, condition pod morphological traits. However, not all them have been mapped or validated nor candidate genes proposed. We sought to investigate the genomic regions conditioning pod morphological and color characters through GWAS.

RESULTS

Single and multi-locus genome wide association analysis was used to investigate pod traits for a set of 301 bean lines of the Spanish Diversity Panel (SDP). The SDP was genotyped with 32,812 SNPs obtained from Genotyping by Sequencing. The panel was grown in two seasons and phenotypic data were recorded for 17 fresh pods traits grouped in four pod characters: pod length, pod cross-section, pod color, and number of seeds per pod. In all, 23 QTL for pod length, 6 for cross-section, 18 for pod color, 6 for number of seeds per pod and 9 associated to two or more pod characters were detected. Most QTL were located in the telomeric region of chromosomes Pv01, Pv02, Pv04, Pv08, Pv09 and Pv10. Eighteen detected QTL co-localized with 28 previously reported QTL. Twenty-one potential candidate genes involving developmental processes were detected underlying 11 QTL for pod morphological characters, four of them homologous to A. thaliana genes FIS2, SPL10, TTG2 and AML4 affecting silique size. Eight potential candidate genes involved in pigment synthesis, were found underlying five QTL for pod color.

CONCLUSIONS

GWAS for pod morphological and color characters in the bean Spanish Diversity Panel revealed 62 QTL, 18 co-localized with previously reported QTL, and 16 QTL were underlain by 25 candidate genes. Overall 44 new QTL identified and 18 existing QTL contribute to a better understanding of the complex inheritance of pod size and color traits in common bean and open the opportunity for future validation works.

Marker association study of yield attributing traits in common bean (Phaseolus vulgaris L.)

Common bean is gaining acceptance as one of the most valuable major food consumed worldwide owing to innumerable nutritional and therapeutic benefits. Comparatively less productivity in underdeveloped countries encouraged us to proceed for QTL mining of yield traits in common bean. Heretofore, multiple yield associated markers have been detected all over the world; even so, the present work is looked on as the first report on identification of novel/new potent markers by exploiting the germplasm of Northern India. A panel of one hundred and thirty five genotypes was used for morphological studies and based on preliminary molecular evaluation; a set of ninety six diverse common bean genotypes (core set) was selected for association analysis. Molecular data generated by a total of ninety eight microsatellite markers (53 genomic and 45 genic SSRs) revealed high estimation of polymorphism among the genotypes that were observed to be divided into two major sub-populations and varying levels of admixtures based on population structure analyses. By employing both MLM and GLM analysis approaches, we identified 46 and 16 significant marker-trait associations (p ≤ 0.005) respectively, few of which have already been reported and hence validate our results. PVBR213 marker was found to be strongly associated with days to bud initiation trait when analyzed with both the approaches. Phenotypic variation of identified significant markers ranged from 3.1% to 32.7% where PVBR87, PVBR213, X96999 and X57022 explain more than 30% of phenotypic variation for 100 seed weight, days to bud initiation, pods per plant and pod length traits respectively. These findings introduce highly informative markers to aid marker-assisted selection program in common bean for high yield performance along with good agronomic merit.

Dataset comparing the growth of fodder crops and soil structure dynamics in an industrial biosludge amended arid soil

The dataset in this work compares the response of two fodder crops, alfalfa (Medicago sativa) and buffel grass (Cenchrus ciliaris), to industrial biosludge amendment of an arid soil in the State of Qatar. It also evaluates the response of soil structure parameters in the biosludge-amended soils containing the different fodder crops. The dataset relates to our previously published works detailed subsequently. The underlying data comparing the water storage capacity and pore structure evolution of the planted soils treated with 0.75, 1.5, and 3% biosludge contents, which showed good outcomes in the companion articles, alongside soil only and soil-fertilizer controls, are presented. These are shown in terms of the percentage of irrigation water leached, and variations in the logarithmic mean T₂ (i.e., T2LM - a proxy for mean pore size) and cumulative porosity, respectively. Data on plant growth parameters such as the number of days to flowering, plant height, and aboveground fresh biomass weight in individual replicates of the different treatments as a percentage of the soil-fertilizer control are also shown. The dataset shows the different responses of both plants and the planted soils to amendments with industrial biosludge from the wastewater treatment plant of a gas-to-liquid (GTL) plant.

Genomic Prediction of Agronomic Traits in Common Bean (Phaseolus vulgaris L.) Under Environmental Stress

In plant and animal breeding, genomic prediction models are established to select new lines based on genomic data, without the need for laborious phenotyping. Prediction models can be trained on recent or historic phenotypic data and increasingly available genotypic data. This enables the adoption of genomic selection also in under-used legume crops such as common bean. Beans are an important staple food in the tropics and mainly grown by smallholders under limiting environmental conditions such as drought or low soil fertility. Therefore, genotype-by-environment interactions (G × E) are an important consideration when developing new bean varieties. However, G × E are often not considered in genomic prediction models nor are these models implemented in current bean breeding programs. Here we show the prediction abilities of four agronomic traits in common bean under various environmental stresses based on twelve field trials. The dataset includes 481 elite breeding lines characterized by 5,820 SNP markers. Prediction abilities over all twelve trials ranged between 0.6 and 0.8 for yield and days to maturity, respectively, predicting new lines into new seasons. In all four evaluated traits, the prediction abilities reached about 50-80% of the maximum accuracies given by phenotypic correlations and heritability. Predictions under drought and low phosphorus stress were up to 10 and 20% improved when G × E were included in the model, respectively. Our results demonstrate the potential of genomic selection to increase the genetic gain in common bean breeding. Prediction abilities improved when more phenotypic data was available and G × E could be accounted for. Furthermore, the developed models allowed us to predict genotypic performance under different environmental stresses. This will be a key factor in the development of common bean varieties adapted to future challenging conditions.

The genetic control of leaf allometry in the common bean, Phaseolus vulgaris

BACKGROUND

To maximize photosynthetic efficiency, plants have evolved a capacity by which leaf area scales allometrically with leaf mass through interactions with the environment. However, our understanding of genetic control of this allometric relationship remains limited.

RESULTS

We integrated allometric scaling laws expressed at static and ontogenetic levels into genetic mapping to identify the quantitative trait loci (QTLs) that mediate how leaf area scales with leaf mass and how such leaf allometry, under the control of these QTLs, varies as a response to environment change. A major QTL detected by the static model constantly affects the allometric growth of leaf area vs. leaf mass for the common bean (Phaseolus vulgaris) in two different environments. The ontogenetic model identified this QTL plus a few other QTLs that determine developmental trajectories of leaf allometry, whose expression is contingent heavily upon the environment.

CONCLUSIONS

Our results gain new insight into the genetic mechanisms of how plants program their leaf morphogenesis to adapt to environmental perturbations.

Seed protein content and its relationships with agronomic traits in pigeonpea is controlled by both main and epistatic effects QTLs

The genetic architecture of seed protein content (SPC) and its relationships to agronomic traits in pigeonpea is poorly understood. Accordingly, five F₂ populations segregating for SPC and four agronomic traits (seed weight (SW), seed yield (SY), growth habit (GH) and days to first flowering (DFF)) were phenotyped and genotyped using genotyping-by-sequencing approach. Five high-density population-specific genetic maps were constructed with an average inter-marker distance of 1.6 to 3.5 cM, and subsequently, integrated into a consensus map with average marker spacing of 1.6 cM. Based on analysis of phenotyping data and genotyping data, 192 main effect QTLs (M-QTLs) with phenotypic variation explained (PVE) of 0.7 to 91.3% were detected for the five traits across the five populations. Major effect (PVE ≥ 10%) M-QTLs included 14 M-QTLs for SPC, 16 M-QTLs for SW, 17 M-QTLs for SY, 19 M-QTLs for GH and 24 M-QTLs for DFF. Also, 573 epistatic QTLs (E-QTLs) were detected with PVE ranging from 6.3 to 99.4% across traits and populations. Colocalization of M-QTLs and E-QTLs explained the genetic basis of the significant (P < 0.05) correlations of SPC with SW, SY, DFF and GH. The nature of genetic architecture of SPC and its relationship with agronomic traits suggest that genomics-assisted breeding targeting genome-wide variations would be effective for the simultaneous improvement of SPC and other important traits.

Characterization of QTL and Environmental Interactions Controlling Flowering Time in Andean Common Bean (Phaseolus vulgaris L.)

Genetic variation for response of flowering time to photoperiod plays an important role in adaptation to environments with different photoperiods, and as consequence is an important contributor to plant productivity and yield. To elucidate the genetic control of flowering time [days to flowering (DTF); growing degree days (GDD)] in common bean, a facultative short-day plant, a quantitative trait loci (QTL) analysis was performed in a recombinant inbred mapping population derived from a cultivated accession and a photoperiod sensitive landrace, grown in different long-day (LD) and short-day (SD) environments by using a multiple-environment QTL model approach. A total of 37 QTL across 17 chromosome regions and 36 QTL-by-QTL interactions were identified for six traits associated with time to flowering and response to photoperiod. The DTF QTL accounted for 28 and 11% on average of the phenotypic variation in the population across LD and SD environments, respectively. Of these, a genomic region on chromosome 4 harboring the major DTF QTL was associated with both flowering time in LD and photoperiod response traits, controlling more than 60% of phenotypic variance, whereas a major QTL on chromosome 9 explained up to 32% of flowering time phenotypic variation in SD. Different epistatic interactions were found in LD and SD environments, and the presence of significant QTL × environment (QE) and epistasis × environment interactions implies that flowering time control may rely on different genes and genetic pathways under inductive and non-inductive conditions. Here, we report the identification of a novel major locus controlling photoperiod sensitivity on chromosome 4, which might interact with other loci for controlling common bean flowering time and photoperiod response. Our results have also demonstrated the importance of these interactions for flowering time control in common bean, and point to the likely complexity of flowering time pathways. This knowledge will help to identify and develop opportunities for adaptation and breeding of this legume crop.

Altered Expression of an FT Cluster Underlies a Major Locus Controlling Domestication-Related Changes to Chickpea Phenology and Growth Habit

Flowering time is a key trait in breeding and crop evolution, due to its importance for adaptation to different environments and for yield. In the particular case of chickpea, selection for early phenology was essential for the successful transition of this species from a winter to a summer crop. Here, we used genetic and expression analyses in two different inbred populations to examine the genetic control of domestication-related differences in flowering time and growth habit between domesticated chickpea and its wild progenitor Cicer reticulatum. A single major quantitative trait locus for flowering time under short-day conditions [Days To Flower (DTF)3A] was mapped to a 59-gene interval on chromosome three containing a cluster of three FT genes, which collectively showed upregulated expression in domesticated relative to wild parent lines. An equally strong association with growth habit suggests a pleiotropic effect of the region on both traits. These results indicate the likely molecular explanation for the characteristic early flowering of domesticated chickpea, and the previously described growth habit locus Hg. More generally, they point to de-repression of this specific gene cluster as a conserved mechanism for achieving adaptive early phenology in temperate legumes.

Parallel origins of photoperiod adaptation following dual domestications of common bean

Common bean (Phaseolus vulgaris L.) is an important grain legume domesticated independently in Mexico and Andean South America approximately 8000 years ago. Wild forms are obligate short-day plants, and relaxation of photoperiod sensitivity was important for expansion to higher latitudes and subsequent global spread. To better understand the nature and origin of this key adaptation, we examined its genetic control in progeny of a wide cross between a wild accession and a photoperiod-insensitive cultivar. We found that photoperiod sensitivity is under oligogenic control, and confirm a major effect of the Ppd locus on chromosome 1. The red/far-red photoreceptor gene PHYTOCHROME A3 (PHYA3) was identified as a strong positional candidate for Ppd, and sequencing revealed distinct deleterious PHYA3 mutations in photoperiod-insensitive Andean and Mesoamerican accessions. These results reveal the independent origins of photoperiod insensitivity within the two major common bean gene pools and demonstrate the conserved importance of PHYA genes in photoperiod adaptation of short-day legume species.

Adapting legume crops to climate change using genomic approaches

Our agricultural system and hence food security is threatened by combination of events, such as increasing population, the impacts of climate change, and the need to a more sustainable development. Evolutionary adaptation may help some species to overcome environmental changes through new selection pressures driven by climate change. However, success of evolutionary adaptation is dependent on various factors, one of which is the extent of genetic variation available within species. Genomic approaches provide an exceptional opportunity to identify genetic variation that can be employed in crop improvement programs. In this review, we illustrate some of the routinely used genomics-based methods as well as recent breakthroughs, which facilitate assessment of genetic variation and discovery of adaptive genes in legumes. Although additional information is needed, the current utility of selection tools indicate a robust ability to utilize existing variation among legumes to address the challenges of climate uncertainty.

Assessing and Exploiting Functional Diversity in Germplasm Pools to Enhance Abiotic Stress Adaptation and Yield in Cereals and Food Legumes

There is a need to accelerate crop improvement by introducing alleles conferring host plant resistance, abiotic stress adaptation, and high yield potential. Elite cultivars, landraces and wild relatives harbor useful genetic variation that needs to be more easily utilized in plant breeding. We review genome-wide approaches for assessing and identifying alleles associated with desirable agronomic traits in diverse germplasm pools of cereals and legumes. Major quantitative trait loci and single nucleotide polymorphisms (SNPs) associated with desirable agronomic traits have been deployed to enhance crop productivity and resilience. These include alleles associated with variation conferring enhanced photoperiod and flowering traits. Genetic variants in the florigen pathway can provide both environmental flexibility and improved yields. SNPs associated with length of growing season and tolerance to abiotic stresses (precipitation, high temperature) are valuable resources for accelerating breeding for drought-prone environments. Both genomic selection and genome editing can also harness allelic diversity and increase productivity by improving multiple traits, including phenology, plant architecture, yield potential and adaptation to abiotic stresses. Discovering rare alleles and useful haplotypes also provides opportunities to enhance abiotic stress adaptation, while epigenetic variation has potential to enhance abiotic stress adaptation and productivity in crops. By reviewing current knowledge on specific traits and their genetic basis, we highlight recent developments in the understanding of crop functional diversity and identify potential candidate genes for future use. The storage and integration of genetic, genomic and phenotypic information will play an important role in ensuring broad and rapid application of novel genetic discoveries by the plant breeding community. Exploiting alleles for yield-related traits would allow improvement of selection efficiency and overall genetic gain of multigenic traits. An integrated approach involving multiple stakeholders specializing in management and utilization of genetic resources, crop breeding, molecular biology and genomics, agronomy, stress tolerance, and reproductive/seed biology will help to address the global challenge of ensuring food security in the face of growing resource demands and climate change induced stresses.