Biology subjects

Gepts, P.

Publications and source records attributed to Gepts, P..

13 recordsLinked to original sources

bioRxiv2026

Novel quantitative trait loci conferring broad-based resistance to root-knot nematodes in lima bean (Phaseolus lunatus)

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. Three 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 and QRk-pl10.1 affected levels of RG and ER of both RKN species, while QRk-pl04.1 suppressed root galling and 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 broad-based RKN resistance in lima beans.

plant biology↗

bioRxiv2026

Genotypic and multi-environment phenotypic evaluation of the lima bean USDA National Plant Germplasm System collection

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.

plant biology↗

bioRxiv2026

Genotypic and environmental effects on seed coat patterning and nutritional composition in common bean (Phaseolus vulgaris L.)

Common bean (Phaseolus vulgaris L.) is the leading grain legume consumed directly by humans and a primary source of nutrients in many communities. This study utilized common bean genotypes with diverse seed coat phenotypes to investigate genotypic and environmental effects on pigmented seed coat area and seed macronutrient (protein, starch, fat, ash, moisture), anti-nutrient (phytate), and mineral nutrient (iron, zinc, calcium, phosphorus, magnesium, potassium, sodium) profiles. Recombinant inbred lines (RILs) that comprise six phenotypic classes for seed coat patterning and nine commercial cultivars were field-evaluated for multiple years across inland, coastal, and intermountain environments in California. A custom near-infrared spectroscopy calibration improved macronutrient prediction accuracy relative to a pre-existing calibration. Environmental effects on macronutrients were pronounced; the 2022 coastal growing environment was the most distinct, characterized by significantly higher starch and moisture content and significantly lower protein content in the RILs relative to any other environments. Across growing years in the RILs, greater consistency was observed at the inland site, where only protein was significantly different; all macronutrient traits significantly differed within the intermountain site. Certain commercial cultivars largely maintained their relative rank for protein content across environments, indicating consistency of genotypic performance, and Black Nightfall ranked among the highest for iron, zinc, phosphorus, and magnesium. Percent pigmented seed coat area was significantly negatively correlated with both calcium and magnesium concentrations. These results underscore the importance of genotype-by-environment field trials for seed coat patterning, seed nutritional composition, and their interplay, to support breeding of common bean among other grain legumes. HighlightsO_LICustom near-infrared spectroscopy (NIRS) calibration improved prediction accuracies C_LIO_LIEnvironmental effects significantly influenced common bean macronutrient composition C_LIO_LICertain cultivars ranked consistently for macronutrient traits across environments C_LIO_LISeed coat pattern was significantly associated with mineral nutrient concentrations C_LI

plant biology↗

bioRxiv2025

Drone methods and educational resources for plant science and agriculture

Technological advances have made drones (UAVs) increasingly important tools for the collection of trait data in plant science. Many costs for the analysis of plant populations have dropped precipitously in recent decades, particularly for genetic sequencing. Similarly, hardware advances have made it increasingly simple and practical to capture drone imagery of plant populations.However, converting this imagery into high-precision and high-throughput tabular data has become a major bottleneck in plant science. Here, we describe high-throughput phenotyping methods for the analysis of numerous plant traits based on imagery from diverse sensor types. Methods can be flexibly combined to extract data related to canopy temperature, area, height, volume, vegetation indices, and summary statistics derived from complex segmentations and classifications. We then describe educational and training resources for these methods, including a web page (PlantScienceDroneMethods.github.io) and an educational YouTube channel (https://www.youtube.com/@travisparkerplantscience) with step-by-step protocols, example data, and example scripts for the whole drone data processing pipeline. These resources facilitate the extraction of high-throughput and high-precision phenomic data, removing barriers to the phenomic analysis of large plant populations.

plant biology↗

bioRxiv2025

A domestication change at PvMYB26 in common bean sheds light on the origins of Middle American agriculture

Domestication imposed radically different selection pressures on plants, eventually transforming them into the cultivated forms that support global populations today. Here, we investigate the loss of seed dispersal via pod shattering during common bean (Phaseolus vulgaris L.) domestication. We identified an eight-kb deletion eliminating the transcription start site and promoter of the candidate gene PvMYB26. Mutants express PvMYB26 at < 1% of the level of wild types and produce 44% less pod lignin. Whole-genome sequencing revealed that the mutation is nearly diagnostic for domestication status among Middle American common bean, indicating its importance in domestication. We also identified a high-frequency PvMYB26 frameshift/premature stop mutation unique to Andean domesticates. Wild haplotypes most like Middle American domesticates are found in eastern Jalisco, Mexico. Our results suggest that West-Central Mexico was the site of common bean domestication and suggest that this region may have been important in the rise of Middle American agriculture.

evolutionary biology↗

bioRxiv2024

An empirical evaluation of simulated gastrointestinal digestion platforms for use in plant breeding, using common bean (Phaseolus vulgaris L.) as a model

There remains a disconnect in plant breeding between increasing nutrient levels in crops at time of harvest and increasing bioaccessible levels of those nutrients during digestion. This study aims to develop and compare simulated digestion models for use in plant breeding and examine bioaccessible nutrient levels in common bean samples with differing seed coat coloration and patterning. The highest trait values (starch and protein hydrolysis, total phenolics, and antioxidant power) were observed from more dynamic digestion models, but even simple dynamic models showed higher trait values than a commonly used static digestion model. The use of these models provided insight on nutrient bioaccessibility; e.g., differences were observed during digestion between common bean genotypes for protein hydrolysis and between growing environments for both total phenolics and protein hydrolysis. Together, these results inform potential future pathways for applying simulated digestion models in plant breeding to improve bioaccessible nutrient levels in crops.

plant biology↗

bioRxiv2024

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 x 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.

plant biology↗

bioRxiv2023

Inbreeding depression leads to reduced fitness in declining populations of wild maize

Crop wild relatives can serve as a source of variation for the genetic improvement of modern varieties. However, the realization of this genetic potential depends critically on the conservation of wild populations. In this study, five populations of Zea mays ssp. parviglumis, the closest relative of domesticated maize, were collected in Jalisco, Mexico and planted in a common garden. Eleven traits related to plant fitness were measured and evaluated in the context of genetic diversity and genetic load. Plants whose seed were sourced from larger, less disturbed populations had greater genetic diversity, lower genetic load, and possessed phenotypes associated with higher fitness, while plants sourced from smaller, heavily impacted populations had traits characteristic of lower fitness and increased genetic load. For example, plants from larger populations germinated more quickly, reached anthesis sooner, demonstrated a higher level of photosynthetic activity, and produced more above-ground biomass, suggesting a direct correlation between the fitness of a population, genetic diversity, and genetic load. These results emphasize the importance of preserving the habitat of populations of Zea mays ssp. parviglumis to limit inbreeding depression and maintain the genetic diversity and adaptive potential of this germplasm.

plant biology↗

bioRxiv2023

Sequence characterization of T, Bip, and Phbw demonstrates the role of MYB-bHLH-WD40 complexes and temperature in common bean seed color pattern formation

Seed colors and color patterns are critical for the survival of wild plants and the consumer appeal of crops. In common bean, a major global staple, these patterns are also critical for determining market classes, yet the genetic and environmental control of many pigmentation patterns remains unresolved. In this study, we genetically mapped variation for three important seed pattern loci, T, Bip, and phbw, which co-segregated completely with PvTTG1, PvMYC1, and PvTT8, respectively. Proteins encoded by these genes are predicted to work together in MYB-bHLH-WD40 (MBW) complexes, propagating flavonoid biosynthesis across the seed coat. Whole-genome sequencing of 37 diverse accessions identified putative mutations in each gene, including seven unique parallel mutations in T (PvTTG1) and a non-synonymous SNP in a conserved residue in bipana (PvMYC1). A 612 bp intron deletion in phbw (PvTT8) eliminated motifs conserved since the origins of the Papilionoidea and corresponded to a 20-fold reduction in transcript abundance. Mutations in MBW candidate genes for Z (PvTT2) and Sellatus (WDR) were also identified. In multi-location field trials with seven varieties with partial seed coat patterning, pigmented seed coat area was highly unstable and correlated with temperature, with up to 11-fold differences in pigmented area between the warmest and the coolest environments. In controlled growth chamber conditions, an increase of 4 {degrees}C was sufficient to cause pigmentation on an additional 21% of the seed coat area. Our results shed light on the fundamental activation of flavonoid biosynthesis in common bean and will be instrumental for maximizing consumer appeal in this nutritious staple crop. Summary- Seed colors and patterns are critical for the survival of wild plants, and are important in differentiating crop market classes, but the genetic control of these in the staple crop common bean (Phaseolus vulgaris) is largely unknown. - The genetic, transcriptional, and environmental basis of common bean seed color patterning was explored through QTL mapping, whole-genome sequencing, RT-qPCR, and automated pigmentation quantification of seed grown in multi-location field trials and growth chamber environments. - MYB-bHLH-WD40 complex-forming genes PvTTG1, PvMYC1, and PvTT8 co-segregated completely with the color patterning genes T, Bip, and phbw. Mutations were identified in each gene, including seven unique parallel mutations in T (PvTTG1), a non-synonymous SNP in a conserved residue in bipana (PvMYC1), and an intron deletion in phbw (PvTT8) eliminating highly conserved motifs and corresponding to 20-fold lower PvTT8 transcript abundance. Mutations in MBW candidate genes Z (PvTT2) and Sellatus (WDR) were also identified. In multi-location field trials, pigmented seed coat area was highly unstable and corresponded to temperature. In growth chamber conditions, an increase of 4 {degrees}C caused pigmentation on an additional 21% of the seed coat area. - Our results highlight the critical interaction between MYB-bHLH-WD40 complex components and temperature in establishing seed pattern diversity.

plant biology↗

bioRxiv2022

Selection and adaptive introgression guided the complex evolutionary history of European common bean

Domesticated crops have been disseminated by humans over vast geographic areas. After 1492, the common bean (Phaseolus vulgaris L.) was introduced in Europe. Here, we combine whole-genome profiling, metabolic fingerprinting and phenotypic characterisation, and we show that the first common bean cultigens successfully introduced into Europe were of Andean origin, after Francisco Pizarros expedition to northern Peru in 1529. We show that hybridisation, selection and recombination have shaped the genomic diversity of the European common bean in parallel with political constraints. There is clear evidence of adaptive introgression into the Mesoamerican-derived European genotypes, with 44 Andean introgressed genomic segments shared by more than 90% of European accessions and distributed across all chromosomes except PvChr11. Genomic scans for signatures of selection highlight the role of genes relevant to flowering and environmental adaptation, suggesting that introgression has been crucial for the dissemination of this tropical crop to the temperate regions of Europe.

genomics↗

bioRxiv2022

Loss of pod strings in common bean is associated with gene duplication, retrotransposon insertion, and overexpression of PvIND

Regulation of fruit development has been central in the evolution and domestication of flowering plants. In common bean (Phaseolus vulgaris L.), a major global staple crop, the two main economic categories are distinguished by differences in fiber deposition in pods: a) dry beans with fibrous and stringy pods; and b) stringless snap/green beans with reduced fiber deposition, but which frequently revert to the ancestral stringy state. To better understand control of this important trait, we first characterized developmental patterns of gene expression in four phenotypically diverse varieties. Then, using isogenic stringless/revertant pairs of six snap bean varieties, we identified strong overexpression of the common bean ortholog of INDEHISCENT (PvIND) in non-stringy types compared to their string-producing counterparts. Microscopy of these pairs indicates that PvIND overexpression is associated with overspecification of weak dehiscence zone cells throughout the entire pod vascular sheath. No differences in PvIND DNA methylation were correlated with pod string phenotype. Sequencing of a 500 kb region surrounding PvIND in the stringless snap bean cultivar Hystyle revealed that PvIND had been duplicated into two tandem repeats, and that a Ty1-copia retrotransposon was inserted between these tandem repeats, possibly driving PvIND overexpression. Further sequencing of stringless/revertant isogenic pairs and diverse materials indicated that these sequence features had been uniformly lost in revertant types and were strongly predictive of pod phenotype, supporting their role in PvIND overexpression and pod string phenotype. SignificanceFruit dehiscence is a key trait for seed dissemination. In legumes, e.g., common bean, dehiscence relies on the presence of fibers, including pod "strings". Selections during domestication and improvement have decreased (dry beans) or eliminated (snap beans) fibers, but reversion to the fibrous state occurs frequently in snap beans. In this article, we document that fiber loss or gain is controlled by structural changes at the PvIND locus, a homolog of the Arabidopsis INDEHISCENT gene. These changes include a duplication of the locus and insertion/deletion of a retrotransposon, which are associated with significant changes in PvIND expression. Our findings shed light on the molecular basis of unstable mutations and provide potential solutions to an important pod quality issue. Competing Interest StatementThe authors have no competing interests.

plant biology↗

bioRxiv2019

Signatures of Environmental Adaptation During Range Expansion of Wild Common Bean (Phaseolus vulgaris)

Landscape genomics integrates population genetics with landscape ecology, allowing the identification of putative molecular determinants involved in environmental adaptation across the natural geographic and ecological range of populations. Wild Phaseolus vulgaris, the progenitor of common bean (P. vulgaris), has a remarkably extended distribution over 10,000 km from northern Mexico to northwestern Argentina. Earlier research has shown that this distribution represents a range expansion from Mesoamerica to the southern Andes through several discrete migration events and that the species colonized areas with different temperature and rainfall compared to its core area of origin. Thus, this species provides an opportunity to examine to what extent adaptation of a species can be broadened or, conversely, ecological or geographical distribution can be limited by inherent adaptedness. In the current study, we applied a landscape genomics approach to a collection of 246 wild common bean accessions representative of its broad geographical and climatic distribution and genotyped for [~]20K SNPs. We applied two different but complementary approaches for identifying loci putatively involved in environmental adaptation: i) an outlier-detection method that identifies loci showing strong differentiation between sub-populations; ii) an association method based on the identification of loci associated with bio-climatic variables. This integrated approach allowed the identification of several genes showing signature of selection across the different natural sub-populations of this species, as well as genes associated with specific bio-climatic variables related to temperature and precipitation. The current study demonstrates the feasibility of landscape genomics approach for a preliminary identification of specific populations and novel candidate genes involved in environmental adaptation in P. vulgaris. As a resource for broadening the genetic diversity of the domesticated gene pool of this species, the genes identified constitute potential molecular markers and introgression targets for the breeding improvement of domesticated common bean.\n\nAuthor SummaryThe ancestral form of common bean has an unusually large distribution in the Americas, extending over 10,000 km from [~]35{degrees} N. Lat. to [~]35{degrees} S. Lat. This wide distribution results from discrete long-range dissemination events to the Andes region from the original environments in Mesoamerica. It also suggests adaptation to new environments that are distinct from those encountered in Mesoamerica. In this research, we identified genes that may be involved in adaptation to climate variables in these new environments using two methods. A first method - outlier detection - was used to identify genome regions that differentiated the wild bean groups in the Andes resulting from discrete dissemination events among themselves and the different groups in Mesoamerica. The second method - genome-wide association - was used to identify candidate genome regions correlated with these same variables across the entire distribution from Mesoamerica to the southern Andes. The two methods identified two sets of candidate genes, several of which were related to the water status of plants, and illustrate how the genetic architecture of adaptation following long-range dissemination. This study provides sets of candidate genes as well as candidate wild bean populations that need to be corroborated for their use in increasing the water use efficiency of domesticated beans.

ecology↗

bioRxiv2019

Genetic control of pod dehiscence in domesticatedcommon bean: Associations with range expansionand local aridity conditions

SignificancePlant domestication has radically modified crop morphology and development. Nevertheless, many crops continue to display some atavistic characteristics that were advantageous to their wild ancestors, such as pod dehiscence (PD). Domesticated common bean (Phaseolus vulgaris), a nutritional staple for millions of people globally, shows considerable variation in PD. Here, we identified multiple genetic regions controlling PD in common bean grown throughout geographically distributed lineages. For example, on chromosome Pv03, PvPdh1 shows a single base-pair substitution that is strongly associated with decreased PD and expansion of the crop into northern Mexico, where the arid conditions promote PD. The environmental dependency and genetic redundancy explain the maintenance of atavistic traits under domestication. Knowledge of PD genetics will assist in developing aridity-adapted varieties.\n\nAbstractA reduction in pod dehiscence (PD) is an important part of the domestication syndrome in legumes, including common bean. Despite this, many modern dry bean varieties continue to suffer yield reductions due to dehiscence, an atavistic trait, which is particularly problematic in hot, dry environments. To date, the genetic control of this important trait has been only partially resolved. Using QTL mapping and GWAS, we identified major PD QTLs in dry beans on chromosomes Pv03, Pv05, Pv08, and Pv09, three of which had not been described previously. We further determined that the QTL on chromosome Pv03, which is strongly associated with PD in Middle American beans, includes a dirigent-like candidate gene orthologous to Pod dehiscence 1 (Pdh1) of soybean. In this gene, we identified a substitution in a highly conserved amino acid that is unique to PD-resistant varieties. This allele is associated with the expansion of Middle American domesticated common beans into the arid environments of northern Mexico, resulting in a high allelic frequency in the domesticated ecogeographic race Durango. The polygenic redundancy and environmental dependency of PD resistance may explain the maintenance of this atavistic characteristic after domestication. Use of these alleles in breeding will reduce yield losses in arid growing conditions, which are predicted to become more widespread in coming decades.

plant biology↗