A robust SNP-haplotype assay for Bct gene region conferring resistance to beet curly top virus in common bean (Phaseolus vulgaris L.)

Strausbaugh, C.A. (2023) A robust SNP-haplotype assay for Bct gene region conferring resistance to beet curly top virus in common bean (Phaseolus vulgaris L.). Frontiers in Plant Science. 14 July 2023. pp. 1-15.

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Abstract

Beet curly top virus (BCTV), which is synonymous with curly top virus (CTV),
causes significant yield loss in common bean (snap and dry beans) cultivars and
several other important crops. Common bean cultivars have been found to be
resistant to CTV, but screening for resistance is challenging due to the cyclical
nature of epidemics and spotty feeding by the leafhopper that vectors the virus.
We used an SNP dataset for the Snap Bean Association Panel (SnAP) agroinoculated
with CTV-Logan (CA/Logan) strain to locate the Bct gene region to a
1.7-Mb interval on chromosome Pv07 using genome-wide association study
(GWAS) analysis. Recombinant lines from the SnAP were used to further narrow
the Bct region to a 58.0-kb interval. A missense SNP (S07_2970381) in candidate
gene Phvul.007G036300 Exonuclease V (EXO5) was identified as the most likely
causal mutation, and it was the most significant SNP detected by GWAS in a dry
bean population (DBP) naturally infected by the CTV-Worland (Wor) strain. Tmshift
assay markers developed for SNP S07_2970381 and two linked SNPs,
S07_2970276 and S07_2966197, were useful for tracking different origins of
the Bct EXO5 candidate gene resistance to CTV in common bean. The three
SNPs identified four haplotypes, with haplotype 3-1 (Haplo3-1) of Middle
American origin associated with the highest levels of CTV resistance. This SNPhaplotype
assay will enable breeders to track resistance sources and to develop
cultivars with better CTV resistance.

Item Type:	Article
NWISRL Publication Number:	1761
Subjects:	Irrigated crops > Bean / dry bean
Depositing User:	Users 11 not found.
Date Deposited:	25 Jul 2023 15:52
Last Modified:	25 Jul 2023 15:52
Item ID:	1801
URI:	https://eprints.nwisrl.ars.usda.gov/id/eprint/1801