Population Genomics of Phaseolus spp.: A Domestication Hotspot

Parker, Travis; Gepts, Paul

doi:10.1007/13836_2021_89

Cited by 8 publications

(5 citation statements)

References 324 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Tepary bean has been domesticated as a crop, and it has been produced from the western Mexican states of Jalisco and Colima to the southwestern United States [ 15 ]. It exhibits many unique and favorable genetic attributes, such as disease resistance [ 16 , 17 ], and possesses higher levels of heat and drought tolerance compared to common bean [ 12 , 13 , 14 , 18 ], as well as tolerance to low soil fertility [ 19 ].…”

Section: Introductionmentioning

confidence: 99%

Physiological Characteristics of Cultivated Tepary Bean (Phaseolus acutifolius A. Gray) and Its Wild Relatives Grown at High Temperature and Acid Soil Stress Conditions in the Amazon Region of Colombia

Suárez

Contreras

Anzola

et al. 2021

Plants

View full text Add to dashboard Cite

Common bean (Phaseolus vulgaris L.) is sensitive to different types of abiotic stresses (drought, high temperature, low soil fertility, and acid soil), and this may limit its adaptation and consequently to its yield under stress. Because of this, a sister species, tepary bean (Phaseolus acutifolius A. Gray), has recently gained attention in breeding for improved abiotic stress tolerance in common bean. In this study, we evaluated the adaptation of 302 accessions of tepary bean (Phaseolus acutifolius A. Gray) and its wild relatives (grouped in four types of tepary bean genetic resource: cultivated, acutifolius regressive, acutifolius wild, tenuifolius wild) when grown under high temperature and acid soil conditions with aluminum toxicity in the Amazon region of Colombia. Our objective was to determine differences among four types of tepary bean genetic resource in their morpho-phenological, agronomic, and physiological responses to combined high temperature and acid soil stress conditions. We found that cultivated P. acutifolius var acutifolius presented a greater number of pods per plant, as well as larger seeds and a greater number of seeds per pod. Some traits, such as root biomass, days to flowering and physiological maturity, specific leaf area, and stomatal density, showed significant differences between types of tepary bean genetic resource, probably contributing to difference in adaptation to combined stress conditions of high temperature and acid soil conditions. The photochemical quenching (qP) was higher in cultivated P. acutifolius var. acutifolius, while energy dissipation by non-photochemical quenching (NPQ) in the form of heat and the coefficient of non-photochemical dissipation (qN) were higher in acutifolius regressive and tenuifolius wild accessions. We have identified 6 accessions of cultivated and 19 accessions of tenuifolius wild that exhibited grain yields above 1800 kg ha−1. These accessions could be suitable to use as parents to improve dry seed production of tepary bean under combined stress conditions of high temperature and acid soil.

show abstract

Section: Introductionmentioning

confidence: 99%

Physiological Characteristics of Cultivated Tepary Bean (Phaseolus acutifolius A. Gray) and Its Wild Relatives Grown at High Temperature and Acid Soil Stress Conditions in the Amazon Region of Colombia

Suárez

Contreras

Anzola

et al. 2021

Plants

View full text Add to dashboard Cite

show abstract

“…Similarly, among all alleles reducing pod shattering in the 40 domesticated legume species, PvIND is unique in its genetic dominance (Parker et al ., 2020b). In common bean, mutations for other key domestication traits such as determinacy, photoperiod insensitivity, loss of seed dormancy, white‐seededness, and reduction in pod shattering were all mediated by loss‐of‐function mutations (Parker & Gepts, 2021). In pea ( Pisum sativum L.), the only other legume species with a loss of pod strings, the stringless allele is recessive (McGee & Baggett, 1992).…”

Section: Discussionmentioning

confidence: 99%

“…(2021), who also identified PvIND among genes differentially expressed between Midas and G12873. The distant relationship between these accessions, which descend from distinct gene pools (Andean vs Middle American, respectively; Parker & Gepts, 2021), necessitated an analysis of gene expression in a controlled genetic background. Our RT‐qPCR results conducted in six isogenic backgrounds demonstrate unequivocally that differential PvIND expression is not only correlated with string deposition but is also qualitatively predictive of string formation among all samples and at both sampled time points (Fig.…”

Section: Discussionmentioning

confidence: 99%

“…Members of the legume family have been independently domesticated at least 40 times (Hammer & Khoshbakht, 2014). Of these, common bean ( Phaseolus vulgaris ) is the largest source of plant protein and micro‐nutrition for direct human consumption (Parker & Gepts, 2021). In wild beans, strongly lignified fibres exist at the pod sutures and inside the pod walls (Supporting Information Fig.…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

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

et al. 2022

Self Cite

View full text Add to dashboard Cite

Fruit development has been central in the evolution and domestication of flowering plants. In common bean (Phaseolus vulgaris), the principal global grain legume staple, two main production categories are distinguished by fibre deposition in pods: dry beans, with fibrous, stringy pods; and stringless snap/green beans, with reduced fibre deposition, which frequently revert to the ancestral stringy state. Here, we identify genetic and developmental patterns associated with pod fibre deposition.Transcriptional, anatomical, epigenetic and genetic regulation of pod strings were explored through RNA-seq, RT-qPCR, fluorescence microscopy, bisulfite sequencing and wholegenome sequencing.Overexpression of the INDEHISCENT ('PvIND') orthologue was observed in stringless types compared with isogenic stringy lines, associated with overspecification of weak dehiscencezone cells throughout the pod vascular sheath. No differences in DNA methylation were correlated with this phenotype. Nonstringy varieties showed a tandemly direct duplicated PvIND and a Ty1-copia retrotransposon inserted between the two repeats. These sequence features are lost during pod reversion and are predictive of pod phenotype in diverse materials, supporting their role in PvIND overexpression and reversible string phenotype.Our results give insight into reversible gain-of-function mutations and possible genetic solutions to the reversion problem, of considerable economic value for green bean production.

show abstract

“…Among grain legume crops, the common bean ( Phaseolus vulgaris L.) is the most important species for direct human consumption (Broughton et al 2003, Parker and Gepts 2021). Consumers and farmers exhibit strong preferences for dry beans with specific colors and patterns (as well as seed shape and size), which together account for the wide diversity of seed types found in common bean and related grain legumes.…”

Section: Introductionmentioning

confidence: 99%

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

Parker,

Bolt,

Williams

et al. 2023

Preprint

Self Cite

View full text Add to dashboard Cite

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 4C 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.

show abstract

Population Genomics of Phaseolus spp.: A Domestication Hotspot

Cited by 8 publications

References 324 publications

Physiological Characteristics of Cultivated Tepary Bean (Phaseolus acutifolius A. Gray) and Its Wild Relatives Grown at High Temperature and Acid Soil Stress Conditions in the Amazon Region of Colombia

Physiological Characteristics of Cultivated Tepary Bean (Phaseolus acutifolius A. Gray) and Its Wild Relatives Grown at High Temperature and Acid Soil Stress Conditions in the Amazon Region of Colombia

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

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

Contact Info

Product

Resources

About