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ARS Home » Pacific West Area » Pullman, Washington » Plant Germplasm Introduction and Testing Research » Research » Publications at this Location » Publication #408239
Research Project: Genetic Resource and Information Management for Pulse, Temperate Forage Legume, Oilseed, Vegetable, Grasses, Sugar, Ornamental, and Other Crops

Location: Plant Germplasm Introduction and Testing Research

Title: Bulked target capture sequencing identified numerous genetic loci associated with alfalfa growth vigor during inbreeding

Author
item PARAJULI, ATIT - Washington State University
item BRUEGGEMAN, ROBERT - Washington State University
item WAGNER, STEVEN - Corteva Agriscience
item Warburton, Marilyn
item Peel, Michael
item Yu, Long-Xi
item See, Deven
item ZHANG, ZHIWU - Washington State University

Submitted to: Preprints
Publication Type: Other
Publication Acceptance Date: 5/12/2023
Publication Date: 5/12/2023
Citation: Parajuli, A., Brueggeman, R., Wagner, S., Warburton, M.L., Peel, M., Yu, L., See, D.R., Zhang, Z. 2023. Bulked target capture sequencing identified numerous genetic loci associated with alfalfa growth vigor during inbreeding. Preprints. https://doi.org/10.20944/preprints202305.0898.v1.
DOI: https://doi.org/10.20944/preprints202305.0898.v1

Interpretive Summary: Alfalfa seed production relies on cross-pollination among different individuals. Self-pollination results seed that produces weak plants. Identifying the genetic basis for this poor performance of plants would allow plant breeders to develop more productive alfalfa. This study examined the DNA of both weak and strong alfalfa plants to identify genes associated with the poor performance. It was found that these genes were associated with genes involved in stress response, defense responses against pathogens, and plant reproduction. The identification of this genetic information will benefit the development of more productive alfalfa by allowing the plant breeder to get rid of those genes that are detrimental to plant growth and performance.

Technical Abstract: Alfalfa primarily produces seeds through cross-pollination among different individuals. Self-pollination results in severe inbreeding depression, such as weak seedlings and termination of growth. Identifying the genetic loci associated with vigorous plant growth could enable the elimination of deleterious alleles and eventually develop inbred alfalfa lines for hybrid production. In this study, 215 alfalfa accessions were self-pollinated for three generations. Within accessions, pairs of weak and strong plants were sampled and bulked for exome sequencing. We extracted individual DNA from 534 plants that included parental clones, strong and weak pairs of plants, and plants selected based on the number of seeds produced. Among them, we formed 42 pools, including 16 with strong plants and 17 with weak plants, 3 top-seeded plants, 3 low-seeded plants, and 3 no-seeded plants. Along with 79 individuals, these pools were sequenced in the target regions covering 112,626 contigs across the entire alfalfa genome. From the 121 samples, (42+79) genotyped, 13.2 million SNPs including indels were generated. After filtering for MAF (>5%), depth (<20X), and no missing genotype and removing indels, a total of 588,136 SNPs were obtained which were used for final analysis. A genome-wide association study was performed and identified 11 genetic loci associated with alfalfa plant growth vigor. The GO analysis generated 12 significantly enriched GO terms. The associated SNPs were on, and near genes involved in stress response, defense responses against pathogens, and plant reproduction. These identified SNPs benefit the development of alfalfa inbred lines by purging the deleterious alleles and biomass improvement through marker-assisted selection.