Version 1
: Received: 11 May 2023 / Approved: 12 May 2023 / Online: 12 May 2023 (07:23:24 CEST)
How to cite:
Parajuli, A.; Brueggeman, R.; Wagner, S.; Warburton, M.; Peel, M.; Yu, L.; See, D.; Zhang, Z. Bulked Target Capture Sequencing Identified Numerous Genetic Loci Associated with Alfalfa Growth Vigor During Inbreeding. Preprints2023, 2023050898. https://doi.org/10.20944/preprints202305.0898.v1
Parajuli, A.; Brueggeman, R.; Wagner, S.; Warburton, M.; Peel, M.; Yu, L.; See, D.; Zhang, Z. Bulked Target Capture Sequencing Identified Numerous Genetic Loci Associated with Alfalfa Growth Vigor During Inbreeding. Preprints 2023, 2023050898. https://doi.org/10.20944/preprints202305.0898.v1
Parajuli, A.; Brueggeman, R.; Wagner, S.; Warburton, M.; Peel, M.; Yu, L.; See, D.; Zhang, Z. Bulked Target Capture Sequencing Identified Numerous Genetic Loci Associated with Alfalfa Growth Vigor During Inbreeding. Preprints2023, 2023050898. https://doi.org/10.20944/preprints202305.0898.v1
APA Style
Parajuli, A., Brueggeman, R., Wagner, S., Warburton, M., Peel, M., Yu, L., See, D., & 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
Chicago/Turabian Style
Parajuli, A., Deven See and Zhiwu Zhang. 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
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.
Biology and Life Sciences, Agricultural Science and Agronomy
Copyright:
This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
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