Genetic variation in a tepary bean (Phaseolus acutifolius A. Gray) diversity panel reveals loci associated with biotic stress resistance

Abstract

Tepary bean (Phaseolus acutifolius A. Gray), indigenous to the arid climates of northern Mexico and the Southwest United States, diverged from common bean (Phaseolus vulgaris L.), approximately 2 million years ago and exhibits a wide range of resistance to biotic stressors. The tepary genome is highly syntenic to the common bean genome providing a foundation for discovery and breeding of agronomic traits between these two crop species. Although a limited number of adaptive traits from tepary bean have been introgressed into common bean, hybridization barriers between these two species required the development of bridging lines to alleviate this barrier. Thus, to fully utilize the extant tepary bean germplasm as both a crop and as a donor of adaptive traits, we developed a diversity panel of 422 cultivated, weedy, and wild tepary bean accessions which were then genotyped and phenotyped to enable population genetic analyses and genome‐wide association studies for their response to a range of biotic stressors. Population structure analyses of the panel revealed eight subpopulations and the differentiation of botanical varieties within P. acutifolius. Genome‐wide association studies revealed loci and candidate genes underlying biotic stress resistance including quantitative trait loci for resistance to weevils, common bacterial blight, Fusarium wilt, and bean common mosaic necrosis virus that can be harnessed not only for tepary bean but also common bean improvement.

Genetic differentiation of a southern Africa tepary bean (Phaseolus acutifolius A Gray) germplasm collection using high-density DArTseq SNP markers

“…The grouping of landraces like Uchokwane (G50) and Zimbabwe landrace (G45) with released and breeding varieties in Clusters 1 and 2 signifies the presence of admixtures that could have arisen due to historical exchanges of seeds through the informal seed system or the exchange of germplasm between breeding programs. The number of subpopulations in our study was slightly lower than the six subpopulations reported by Bornowski et al [ 35 ]. This could be attributed to differences in the diversity panels and genotyping platform used.…”

“…arisen due to historical exchanges of seeds through the informal seed system or the exchange of germplasm between breeding programs. The number of subpopulations in our study was slightly lower than the six subpopulations reported by Bornowski et al [35]. This could be attributed to differences in the diversity panels and genotyping platform used.…”

“…Genetic diversity and population structures were examined in Interspecific Mesoamerican X Wild Tepary (IMAWT) population using GBS with high-density SNP markers aligned to the common bean reference genome [ 5 ]. Further, GBS with high-density SNP markers mapped to the tepary bean reference genome in a tepary bean diversity panel has been used to determine the extent of genetic diversity and population structure [ 35 ]. Nevertheless, the southern Africa tepary bean diversity panel collection, comprising landraces, released lines, and breeding lines, has not yet been characterized with high-density DArTSeq SNP markers matched to the tepary bean reference genome.…”

Release of tepary bean cultivar ‘USDA Fortuna’ with improved disease and insect resistance, seed size, and culinary quality

“…The original cross in the development of USDA Fortuna (tested as TARS-Tep 93), G40022 (TDP-13)/G40029 (TDP-18), was completed in a screenhouse at the Tropical Agriculture Research Station (TARS) in Mayaguez, Puerto Rico (PR), in 2014, and parents were selected out of the Tepary Diversity Panel (TDP) (Bornowski et al, 2023) (Miklas et al, 1994), common bacterial blight resistance (Urrea et al, 1999), heat tolerance (Rainey & Griffiths, 2005), and a small yellow round seed type. G40022 was collected by Howard Scott Gentry in 1966 in Newfields, AZ, along the U.S.-Mexico border, at approximately 816 m asl.…”

Inheritance of the Resistance to Acanthoscelides obtectus (Say.) in a Heterogeneous Inbred Families Population of Common Bean (Phaseolus vulgaris L.)

“…Consequently, little is known about the inheritance and mechanisms responsible for resistance or tolerance to A. obtectus in common beans. Only three QTL mapping reports [5,12,13], and two inheritance studies have been reported in biparental crosses, comprising a segregation 15S: 1R by Kornegay and Cardona [8] and 3R: 1S by Jiménez-Galindo et al [14]. In the first study of QTLs, the authors found three QTLs to have resistance against A. obtectus on chromosomes Pv04 and Pv06.…”