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 »
- Authors:
-
- Beltsville Agricultural Research Center-West, MD (United States); USDA-ARS, Beltsville, MD (United States)
- USDA-ARS, Beltsville, MD (United States)
- USDA-ARS, Beltsville, MD (United States); Univ. of Nebraska, Lincoln, NE (United States)
- Univ. of Maryland, College Park, MD (United States)
- North Dakota State Univ., Fargo, ND (United States)
- Univ. of Maryland, College Park, MD (United States); Joint Genome Inst., Walnut Creek, CA (United States)
- 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 Laboratory (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. doi: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 = {Fri Aug 28 00:00:00 EDT 2015},
month = {Fri Aug 28 00:00:00 EDT 2015}
}
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Root and shoot variation in relation to potential intermittent drought adaptation of Mesoamerican wild common bean (Phaseolus vulgaris L.)
journal, December 2018
- Berny Mier y. Teran, Jorge C.; Konzen, Enéas R.; Medina, Viviana
- Annals of Botany, Vol. 124, Issue 6
Accelerating genetic gains in legumes for the development of prosperous smallholder agriculture: integrating genomics, phenotyping, systems modelling and agronomy
journal, March 2018
- Varshney, Rajeev K.; Thudi, Mahendar; Pandey, Manish K.
- Journal of Experimental Botany, Vol. 69, Issue 13
In-depth genome characterization of a Brazilian common bean core collection using DArTseq high-density SNP genotyping
journal, May 2017
- Valdisser, Paula A. M. R.; Pereira, Wendell J.; Almeida Filho, Jâneo E.
- BMC Genomics, Vol. 18, Issue 1
Genetics and mapping of a new anthracnose resistance locus in Andean common bean Paloma
journal, April 2017
- de Lima Castro, Sandra Aparecida; Gonçalves-Vidigal, Maria Celeste; Gilio, Thiago Alexandre Santana
- BMC Genomics, Vol. 18, Issue 1
Agronomic Performance and Nitrogen Fixation of Heirloom and Conventional Dry Bean Varieties Under Low-Nitrogen Field Conditions
journal, July 2019
- Wilker, Jennifer; Navabi, Alireza; Rajcan, Istvan
- Frontiers in Plant Science, Vol. 10
Marker-Assisted Breeding for Economic Traits in Common Bean
book, January 2018
- Kelly, James D.; Bornowski, Nolan
- Biotechnologies of Crop Improvement, Volume 3
De novo hybrid assembly of the rubber tree genome reveals evidence of paleotetraploidy in Hevea species
journal, February 2017
- Pootakham, Wirulda; Sonthirod, Chutima; Naktang, Chaiwat
- Scientific Reports, Vol. 7, Issue 1
Effect of drought stress on the genetic architecture of photosynthate allocation and remobilization in pods of common bean (Phaseolus vulgaris L.), a key species for food security
journal, April 2019
- Berny Mier y. Teran, Jorge C.; Konzen, Enéas R.; Palkovic, Antonia
- BMC Plant Biology, Vol. 19, Issue 1