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ARS Home » Pacific West Area » Pullman, Washington » Grain Legume Genetics Physiology Research » Research » Publications at this Location » Publication #333023

Research Project: Genetic Improvement of Cool Season Food Legumes

Location: Grain Legume Genetics Physiology Research

Title: Genome-wide SNP identification, linkage map construction and QTL mapping for mineral nutrient concentrations and contents in pea (Pisum sativum L.)

Author
item Ma, Yu - Washington State University
item Grusak, Michael
item Cheng, Peng - University Of Missouri
item Mazourek, Michael - Cornell University - New York
item Coyne, Clarice - Clare
item Main, Dorrie - Washington State University
item Mcgee, Rebecca

Submitted to: Biomed Central (BMC) Plant Biology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 12/20/2016
Publication Date: 2/13/2017
Citation: Ma, Y., Grusak, M.A., Cheng, P., Mazourek, M., Coyne, C.J., Main, D., McGee, R.J. 2017. Genome-wide SNP identification, linkage map construction and QTL mapping for mineral nutrient concentrations and contents in pea (Pisum sativum L.). Biomed Central (BMC) Plant Biology. doi: 10.1186/s12870-016-0956-4.

Interpretive Summary: DNA marker-assisted breeding is now routinely used in major crops to facilitate more efficient new crop cultivar improvement. While rich in a variety of nutritional components, such as protein, mineral nutrients, carbohydrates and several vitamins, pea (Pisum sativum L.), one of the oldest consumed foods in the world, remains behind many other crops in the availability of genomic and genetic resources. To further improve mineral nutrient levels in pea seed for human consumption requires the development of DNA markers. The objectives of this research are to develop these tools by: identifying genome-wide DNA markers using modern technology; constructing a high-density linkage map and comparative maps with other legumes, and identifying genes controlling high levels of mineral nutrients in pea seed (boron, calcium, iron, potassium, magnesium, manganese, molybdenum, phosphorous, sulfur, and zinc). In this study, 1,609 useful DNA markers were identified and gene regions were identified controlling high levels of mineral nutrients found in pea seed. The DNA markers and the genetic linkage map developed in this study permitted the identification of specific regions responsible for these high levels of mineral nutrient content in pea seed. Breeders will now be able to use this technology to improve the speed and efficiency of identifying superior pea lines with high levels of important mineral nutrients in the pea seed.

Technical Abstract: Marker-assisted breeding is now routinely used in major crops to facilitate more efficient cultivar improvement. This has been significantly enabled by the use of next-generation sequencing technology to identify loci and markers associated with traits of interest. While rich in a variety of nutritional components, such as protein, mineral nutrients, carbohydrates and several vitamins, pea (Pisum sativum L.), one of the oldest domesticated crops in the world, remains behind many other crops in the availability of genomic and genetic resources. To further improve mineral nutrient levels in pea requires the development of genome-wide tools. The objectives of this research are to develop these tools by: identifying genome-wide single nucleotide polymorphisms (SNPs) using genotyping by sequencing (GBS); constructing a high-density linkage map and comparative maps with other legumes, and identifying quantitative trait loci (QTL) for boron, calcium, iron, potassium, magnesium, manganese, molybdenum, phosphorous, sulfur, and zinc. In this study, 1,609 high quality SNPs were found to be polymorphic between Kiflica and Aragorn, two parents of an F6-derived recombinant inbred line (RIL) population. Mapping 1,683 markers including 75 previously published markers and 1,608 SNPs developed from the present study generated a linkage map of size 1310.1 cM. As expected the highest levels of synenty were observed between pea and the genome of Medicago truncatula. QTL analysis of the RIL population across two locations revealed at least 1 QTL for each of the mineral nutrient trait. In total 51 seed nutrient concentration QTLs, 53 seed nutrient content QTLs, and 6 seed weight QTLs were discovered. The QTLs explained from 2% to 43.3% of the phenotypic variance. The SNPs and the genetic linkage map developed in this study permitted QTL identification for pea mineral nutrients. This represents the first QTL study of mineral nutrient concentration and content in a pea RIL population. The development of a genetic linkage map and genome wide SNPs provides an important resource to enable marker-assisted selection (MAS) in pea breeding programs.