Bao-Lam Huynh

Lima bean (Phaseolus lunatus) is a broadly adapted, economically important leguminous crop and a susceptible host of root-knot nematodes ( Meloidogyne spp.; RKN), which are a devastating plant pathogen in agricultural systems worldwide. To date, there have been few studies to elucidate the genetic determinants of RKN resistance in lima beans. Understanding the genetic mechanisms underlying resistance is essential for improving resistance traits and incorporating them into lima bean breeding programs. To assist in marker-assisted selection, we aimed to identify and map quantitative trait loci (QTLs) conferring RKN resistance-related traits. Three recombinant inbred line (RIL) populations were used in this study. The RIL populations were derived by crossing two RKN-resistant parents with the same RKN-susceptible parent and with each other. All populations were genotyped using genome-wide single-nucleotide polymorphism (SNP) markers. Each population was screened for root galling (RG) and RKN egg reproduction (ER) in response to M. incognita and M. javanica in greenhouse experiments. Three major QTLs were detected and mapped on chromosome Pl04 ( QRk-pl04.1 ), Pl05 ( QRk-pl05.1 ) and Pl10 ( QRk-pl10.1 ) across populations. Among them, QRk-pl05.1 affected RG and ER in response to both RKN species, while QRk-pl04.1 and QRk-pl10.1 suppressed root galling and/or reproduction responses of M. incognita but not of M. javanica . These chromosomal regions defined by flanking markers will help guide marker-assisted breeding and gene discovery for RKN resistance in lima beans.

Summary: Cowpea ( Vigna unguiculata [L.] Walp.) is a resilient grain legume and an important global source of dietary protein, yet the genetic and environmental basis of phenological and canopy development, as well as grain composition, remains incompletely characterized across production environments. In this study, we evaluated a cowpea multi-parent advanced generation intercross (MAGIC) population along an environmental gradient in California (with contrasting daylengths, temperatures, and soil types) using agronomic, grain compositional, and uncrewed aerial vehicle (UAV) and rover-enabled phenotyping. Near-infrared spectroscopy (NIRS) enabled assessment of grain compositional traits, while sensing-enabled time-series imaging captured canopy and reproductive dynamics. Quantitative trait locus (QTL) mapping identified 267 QTL, and genome-wide association studies (GWAS) detected 1,973 marker-trait associations. Integrating QTL mapping and GWAS results identified two major genomic hotspots affecting multiple traits. A chromosome 9 hotspot (5.8–6.0 Mb) was associated with flowering time and co-localized with sensing-enabled measures of flower and pod counts, plant height, and vegetation fraction, indicating broad effects on phenological and canopy development. A chromosome 8 hotspot (37.3–37.9 Mb) contained co-localized signals for seed weight, protein, starch, phytate, and moisture. A total of 22 prioritized candidate genes were identified within these and other loci with multi-environment QTL and GWAS support. Genomic predictive abilities were moderate to high for most traits and scenarios, with multi-trait MegaLMM outperforming RR-BLUP. Together, these results define major genomic regions controlling cowpea phenology, canopy development, and grain composition, and provide targets and strategies for breeding cowpea cultivars with favorable and environmentally resilient productivity and grain composition. Significance Statement: To dissect the genetic basis of cowpea productivity, adaptation, and grain composition, and how performance for these traits varies and can be predicted across environments, we combined multi-environment phenotyping, including sensing of canopy and reproductive traits, with quantitative genetic analyses in a multi-parental population. We identified genomic hotspots for seed size/composition and reproductive phenology and an across-environment predictive advantage for multi-trait vs. single-trait genomic prediction. Overall, these findings support the comprehensive improvement of cowpea.

Lima bean ( Phaseolus lunatus L.) is an economically and agronomically important grain legume. Lima beans (or limas) show a range of climatic adaptations with independent domestications in the Andes (large-seeded) and Mesoamerica (small- or medium-seeded). We generated and integrated genotypic and comprehensive field- and laboratory-based phenotypic information for the available accessions in the USDA National Plant Germplasm System collection across multiple environments to inform germplasm utilization in breeding. A total of 810 accessions were genotyped using short-read, low-coverage sequencing. Accession geographic origin and domestication explained population structure. A partially overlapping subset of the panel ( n =141-308) was field-evaluated across two years in each of Davis, CA, Central Ferry, WA, and Coachella Valley, CA (the latter was fall-planted for evaluation of photoperiod-sensitive accessions) to assess trait performance in contrasting environments. Agronomic traits such as determinacy and flowering time, and seed traits such as seed coat color and hundred-seed weight, were scored. Macronutrient traits (protein, starch, fat, and ash content) were measured on dry (mature) harvested grain via near-infrared spectroscopy. Genome-wide association analyses identified loci significantly associated with descriptive, agronomic, and seed traits, including orthologs of known genes in common bean and novel candidate regions. Genomic predictive abilities were moderate to high for key traits. Finally, we established a conditional core collection that was constrained to include 211 extensively phenotyped accessions and for which 91 supplemental accessions were selected to maximize genetic diversity from among the genotyped accessions. Overall, these resources provide a foundation to support genomics-assisted breeding of limas.

Background/Objectives: Cowpea is an important legume crop in sub-Saharan Africa (SSA) and beyond. However, access to phosphorus (P), a critical element for plant growth and development, is a significant constraint in SSA. Thus, it is essential to have high P-use efficiency varieties to achieve increased yields in environments where little-to- no phosphate fertilizers are applied. Methods: In this study, crop phenology, yield, and grain P efficiency traits were assessed in two recombinant inbred line (RIL) populations across ten environments under high- and low-P soil conditions to identify traits’ response to different soil P levels and associated quantitative trait loci (QTLs). Single-environment (SEA) and multi-environment (MEA) QTL analyses were conducted for days to flowering (DTF), days to maturity (DTM), biomass yield (BYLD), grain yield (GYLD), grain P-use efficiency (gPUE) and grain P-uptake efficiency (gPUpE). Results: Phenotypic data indicated significant variation among the RILs, and inadequate soil P had a negative impact on flowering, maturity, and yield traits. A total of 40 QTLs were identified by SEA, with most explaining greater than 10% of the phenotypic variance, indicating that many major-effect QTLs contributed to the genetic component of these traits. Similarly, MEA identified 23 QTLs associated with DTF, DTM, GYLD, and gPUpE under high- and low-P environments. Thirty percent (12/40) of the QTLs identified by SEA were also found by MEA, and some of those were identified in more than one P environment, highlighting their potential in breeding programs targeting PUE. QTLs on chromosomes Vu03 and Vu08 exhibited consistent effects under both high- and low-P conditions. In addition, candidate genes underlying the QTL regions were identified. Conclusions: This study lays the foundation for molecular breeding for PUE and contributes to understanding the genetic basis of cowpea response in different soil P conditions. Some of the identified genomic loci, many being novel QTLs, could be deployed in marker-aided selection and fine mapping of candidate genes.

Development of high yielding cowpea varieties coupled with good taste and rich in essential minerals can promote consumption and thus nutrition and profitability. The sweet taste of cowpea grain is determined by its sugar content, which comprises mainly sucrose and galacto-oligosaccharides (GOS) including raffinose and stachyose. However, GOS are indigestible and their fermentation in the colon can produce excess intestinal gas, causing undesirable bloating and flatulence. In this study, we aimed to examine variation in grain sugar and mineral concentrations, then map quantitative trait loci (QTLs) and estimate genomic-prediction (GP) accuracies for possible application in breeding. Grain samples were collected from a multi-parent advanced generation intercross (MAGIC) population grown in California during 2016–2017. Grain sugars were assayed using high-performance liquid chromatography. Grain minerals were determined by inductively coupled plasma–optical emission spectrometry and combustion. Considerable variation was observed for sucrose (0.6–6.9%) and stachyose (2.3–8.4%). Major QTLs for sucrose (QSuc.vu-1.1), stachyose (QSta.vu-7.1), copper (QCu.vu-1.1) and manganese (QMn.vu-5.1) were identified. Allelic effects of major sugar QTLs were validated using the MAGIC grain samples grown in West Africa in 2017. GP accuracies for minerals were moderate (0.4–0.58). These findings help guide future breeding efforts to develop mineral-rich cowpea varieties with desirable sugar content.

Long bean (Vigna unguiculata subsp. sesquipedalis, asparagus bean, Asian yardlong bean), the vegetable type of cowpea [Vigna unguiculata (L.) Walp], is a climate‐resilient and nutritious food legume grown by Southeast Asian farmers in the Central Valley of California and marketed to Asian immigrant communities across the United States. Insect pests are major threats, reducing yield and quality of all current lines. Modern plant breeding protocols and extension activities were implemented to develop resistant lines using sources of natural resistance found in African cowpea germplasm. Three aphid‐resistant long bean lines, Dark Green 1994 (Reg no. GP‐320, PI 702995), Light Green 2055 (Reg. no. GP‐321, PI 702996), and Purple 2056 (Reg. no. GP‐322, PI 702997), were developed by introgression of two known quantitative trait loci (QTL) for aphid resistance into three local elite lines through marker‐assisted backcrossing (MABC). One bush‐type long bean line, Bush 2074 (Reg. no. GP‐319, PI 702994), carrying two known QTL for root‐knot nematode resistance, was also developed to enable scaling up production and to improve nematode management in large‐scale commercial farming. These improved lines were evaluated in controlled experiments which also served in outreach activities to enable adoption. Each of these advanced lines, when forming a near‐isogenic pair with its recurrent parent, can provide useful genetic materials for resistance gene discovery.

Consumer preferences for cooking-related traits are a deciding factor in the success of new cowpea [Vigna unguiculata (L.) Walp] cultivars. Pigment leaching is an undesirable trait for both consumers and producers alike that occurs during the cooking or canning process and has been a goal for improvement efforts through breeding. This study leverages the power of bulked segregant analysis to identify a locus segregating for the pigment-leaching trait in an F2 population of blackeye seed-type cowpea. A single major locus was identified on Vu06 spanning 1.27 Mb, and SNP haplotypes were identified for low and high pigment-leaching bulks. However, further evaluation of accessions that are unrelated to the F2 population or its progenitors suggests that the trait is polygenic, such that low or high leakage is not determined solely by this locus. Parallels were drawn between cowpea and a close relative, black bean (Phaseolus vulgaris L.), to suggest that additional seed coat or cooking-related traits may also be involved in the pigment-leaching trait.

‘California Blackeye 77’ (CB77) (Reg. no. CV‐344, PI 698656) is a blackeye‐type cowpea [Vigna unguiculata (L.) Walp] cultivar developed by the University of California, Riverside. CB77 is distinguished from the industry standard cultivars, ‘California Blackeye 46’ (CB46) and ‘California Blackeye 5’ (CB5), by its ability to resist infestation caused by cowpea aphid (Aphis craccivora Koch), a destructive sap‐sucking insect pest prevalent in the Central Valley of California and warm‐to‐hot regions worldwide. CB77 was developed by introgression of two known quantitative trait loci for aphid resistance from the African cowpea breeding line IT97K‐556‐6 into CB46 through marker‐assisted backcrossing. Genotyping with 51,128 single nucleotide polymorphism markers reveals that CB77 is near‐isogenic to CB46 and carries two resistance haplotypes (∼4 Mb in total) from IT97K‐556‐6. On‐station and on‐farm trials with aphid infestations confirmed the inherent resistance in CB77 (aphids covered 0–10% of plant surface area without causing any crown damage, whereas check CB46 had aphids covering 60–70% of plant surface area and causing severe crown damage). Under protected conditions, CB77 showed grain yield, seed quality, and other agronomic characteristics equivalent to CB46 and better yield than CB5. CB77 could therefore be substituted for CB46 and CB5 in production regions where aphids are present. The near‐isogenic pair CB77 and CB46 are also useful materials for resistance gene discovery.

Cowpea is a nutrient-dense legume that significantly contributes to the population’s diet in sub-Saharan Africa and other regions of the world. Improving cowpea cultivars to be more resilient to abiotic stress such as drought would be of great importance. The use of a multi-parent advanced generation intercross (MAGIC) population has been shown to be efficient in increasing the frequency of rare alleles that could be associated with important agricultural traits. In addition, drought tolerance index has been reported to be a reliable parameter for assessing crop tolerance to water-deficit conditions. Therefore, the objectives of this study were to evaluate the drought tolerance index for plant growth habit, plant maturity, flowering time, 100-seed weight, and grain yield in a MAGIC cowpea population, to conduct genome-wide association study (GWAS) and identify single nucleotide polymorphism (SNP) markers associated with the drought tolerance indices, to investigate the potential relationship existing between the significant loci associated with the drought tolerance indices, and to conduct genomic selection (GS). These analyses were performed using the existing phenotypic and genotypic data published for the MAGIC population which consisted of 305 F8 recombinant inbred lines (RILs) developed at University of California, Riverside. The results indicated that: (1) large variation in drought tolerance indices existed among the cowpea genotypes, (2) a total of 14, 18, 5, 5, and 35 SNPs were associated with plant growth habit change due to drought stress, and drought tolerance indices for maturity, flowering time, 100-seed weight, and grain yield, respectively, (3) the network-guided approach revealed clear interactions between the loci associated with the drought tolerance traits, and (4) the GS accuracy varied from low to moderate. These results could be applied to improve drought tolerance in cowpea through marker-assisted selection (MAS) and genomic selection (GS). To the best of our knowledge, this is the first report on marker loci associated with drought tolerance indices in cowpea.

The cowpea [Vigna unguiculata (L.) Walp] multiparent advanced generation intercross (MAGIC) population (Reg. No. MP‐1, NSL 526803 MAP) consists of 305 recombinant inbred lines (RILs). The population was constructed from eight elite parents that are genetically diverse and carry combinations of abiotic and biotic stress resistance traits relevant to cowpea improvement in sub‐Saharan Africa. The eight parents were intermated using structured crosses to ensure the population would have balanced representation from each of the founder parents, followed by seven rounds of single‐seed descent. The resulting F₈ RILs each carry a mosaic of genome blocks contributed from all founders as revealed by high‐resolution single nucleotide polymorphism genotyping. The RILs are diverse in agronomic traits, including flowering time, growth habit, maturity, yield potential, and seed characteristics across environments. Due to its broad genetic base, this cowpea MAGIC population will simplify and facilitate community‐wide discovery of marker‐trait associations and fine mapping for gene discovery.