skip to main content

DOE PAGESDOE PAGES

Title: SNP Assay Development for Linkage Map Construction, Anchoring Whole-Genome Sequence, and Other Genetic and Genomic Applications in Common Bean

A total of 992,682 single-nucleotide polymorphisms (SNPs) was identified as ideal for Illumina Infinium II BeadChip design after sequencing a diverse set of 17 common bean (Phaseolus vulgaris L) varieties with the aid of next-generation sequencing technology. From these, two BeadChips each with >5000 SNPs were designed. The BARCBean6K_1 BeadChip was selected for the purpose of optimizing polymorphism among market classes and, when possible, SNPs were targeted to sequence scaffolds in the Phaseolus vulgaris 14× genome assembly with sequence lengths >10 kb. The BARCBean6K_2 BeadChip was designed with the objective of anchoring additional scaffolds and to facilitate orientation of large scaffolds. Analysis of 267 F2 plants from a cross of varieties Stampede × Red Hawk with the two BeadChips resulted in linkage maps with a total of 7040 markers including 7015 SNPs. With the linkage map, a total of 432.3 Mb of sequence from 2766 scaffolds was anchored to create the Phaseolus vulgaris v1.0 assembly, which accounted for approximately 89% of the 487 Mb of available sequence scaffolds of the Phaseolus vulgaris v0.9 assembly. A core set of 6000 SNPs (BARCBean6K_3 BeadChip) with high genotyping quality and polymorphism was selected based on the genotyping of 365 dry bean and 134more » snap bean accessions with the BARCBean6K_1 and BARCBean6K_2 BeadChips. The BARCBean6K_3 BeadChip is a useful tool for genetics and genomics research and it is widely used by breeders and geneticists in the United States and abroad.« less
Authors:
 [1] ;  [2] ;  [3] ;  [4] ;  [4] ;  [2] ;  [5] ;  [6] ;  [7] ;  [5] ;  [2]
  1. Beltsville Agricultural Research Center-West, MD (United States); USDA-ARS, Beltsville, MD (United States)
  2. USDA-ARS, Beltsville, MD (United States)
  3. USDA-ARS, Beltsville, MD (United States); Univ. of Nebraska, Lincoln, NE (United States)
  4. Univ. of Maryland, College Park, MD (United States)
  5. North Dakota State Univ., Fargo, ND (United States)
  6. Univ. of Maryland, College Park, MD (United States); Joint Genome Inst., Walnut Creek, CA (United States)
  7. Univ. of Georgia, Athens, GA (United States)
Publication Date:
OSTI Identifier:
1239819
Grant/Contract Number:
AC02-05CH11231
Type:
Accepted Manuscript
Journal Name:
G3
Additional Journal Information:
Journal Volume: 5; Journal Issue: 11; Journal ID: ISSN 2160-1836
Publisher:
Genetics Society of America
Research Org:
National Inst. of Food and Agriculture, Washington, DC (United States); U.S. Department of Agriculture, Washington, DC (United States)
Sponsoring Org:
USDOE Office of Science (SC)
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES Phaseolus vulgaris; SNP; molecular markers; BARCBean 6K Bead Chip; linkage map