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

Abstract

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:
Research Org.:
National Inst. of Food and Agriculture, Washington, DC (United States); U.S. Department of Agriculture, Washington, DC (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER)
OSTI Identifier:
1239819
Alternate Identifier(s):
OSTI ID: 1616043
Grant/Contract Number:  
AC02-05CH11231
Resource 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
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; Phaseolus vulgaris; SNP; molecular markers; BARCBean 6K Bead Chip; linkage map

Citation Formats

Song, Qijian, Jia, Gaofeng, Hyten, David L., Jenkins, Jerry, Hwang, Eun-Young, Schroeder, Steven G., Osorno, Juan M., Schmutz, Jeremy, Jackson, Scott A., McClean, Phillip E., and Cregan, Perry B.. SNP Assay Development for Linkage Map Construction, Anchoring Whole-Genome Sequence, and Other Genetic and Genomic Applications in Common Bean. United States: N. p., 2015. Web. https://doi.org/10.1534/g3.115.020594.
Song, Qijian, Jia, Gaofeng, Hyten, David L., Jenkins, Jerry, Hwang, Eun-Young, Schroeder, Steven G., Osorno, Juan M., Schmutz, Jeremy, Jackson, Scott A., McClean, Phillip E., & Cregan, Perry B.. SNP Assay Development for Linkage Map Construction, Anchoring Whole-Genome Sequence, and Other Genetic and Genomic Applications in Common Bean. United States. https://doi.org/10.1534/g3.115.020594
Song, Qijian, Jia, Gaofeng, Hyten, David L., Jenkins, Jerry, Hwang, Eun-Young, Schroeder, Steven G., Osorno, Juan M., Schmutz, Jeremy, Jackson, Scott A., McClean, Phillip E., and Cregan, Perry B.. Fri . "SNP Assay Development for Linkage Map Construction, Anchoring Whole-Genome Sequence, and Other Genetic and Genomic Applications in Common Bean". United States. https://doi.org/10.1534/g3.115.020594. https://www.osti.gov/servlets/purl/1239819.
@article{osti_1239819,
title = {SNP Assay Development for Linkage Map Construction, Anchoring Whole-Genome Sequence, and Other Genetic and Genomic Applications in Common Bean},
author = {Song, Qijian and Jia, Gaofeng and Hyten, David L. and Jenkins, Jerry and Hwang, Eun-Young and Schroeder, Steven G. and Osorno, Juan M. and Schmutz, Jeremy and Jackson, Scott A. and McClean, Phillip E. and Cregan, Perry B.},
abstractNote = {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 134 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.},
doi = {10.1534/g3.115.020594},
journal = {G3},
number = 11,
volume = 5,
place = {United States},
year = {2015},
month = {8}
}

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