Filtering for SNPs with high selective constraint augments mid-parent heterosis predictions in wheat (Triticum aestivum L.)
To extend the contemporary understanding into the grain yield heterosis of wheat, the current study investigated the contribution of deleterious alleles in shaping mid-parent heterosis (MPH). These alleles occur at low frequency in the genome and are often missed by automated genotyping platforms li...
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KeAi Communications Co., Ltd.
2023-02-01
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| Series: | Crop Journal |
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S221451412200157X |
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| author | Abhishek Gogna Jie Zhang Yong Jiang Albert W. Schulthess Yusheng Zhao Jochen C. Reif |
| author_facet | Abhishek Gogna Jie Zhang Yong Jiang Albert W. Schulthess Yusheng Zhao Jochen C. Reif |
| author_sort | Abhishek Gogna |
| collection | DOAJ |
| description | To extend the contemporary understanding into the grain yield heterosis of wheat, the current study investigated the contribution of deleterious alleles in shaping mid-parent heterosis (MPH). These alleles occur at low frequency in the genome and are often missed by automated genotyping platforms like SNP arrays. The deleterious alleles herein were detected using a quantitative measurement of evolutionary conservation based on the phylogeny of wheat and investigations were made to: (1) assess the benefit of including deleterious alleles into MPH prediction models and (2) understand the genetic underpinnings of deleterious SNPs for grain yield MPH using contrasting crosses viz. elite × elite (Exp. 1) and elite × plant genetic resources (PGR; Exp. 2). In our study, we found a lower allele frequency of moderately deleterious alleles in elites compared to PGRs. This highlights the role of purifying selection for the development of elite wheat cultivars. It was shown that deleterious alleles are informative for MPH prediction models: modelling their additive-by-additive effects in Exp. 1 and dominance as well as associated digenic epistatic effects in Exp. 2 significantly boosts prediction accuracies of MPH. Furthermore, heterotic- quantitative trait loci’s underlying MPH was investigated and their properties were contrasted in the two crosses. Conclusively, it was proposed that incomplete dominance of deleterious alleles contributes to grain yield heterosis in elite crosses (Exp. 1). |
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| id | doaj.art-a44a1e1286ba4d5abcb90b30412e30d0 |
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| issn | 2214-5141 |
| language | English |
| last_indexed | 2024-04-10T21:10:07Z |
| publishDate | 2023-02-01 |
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| series | Crop Journal |
| spelling | doaj.art-a44a1e1286ba4d5abcb90b30412e30d02023-01-21T04:21:00ZengKeAi Communications Co., Ltd.Crop Journal2214-51412023-02-01111166176Filtering for SNPs with high selective constraint augments mid-parent heterosis predictions in wheat (Triticum aestivum L.)Abhishek Gogna0Jie Zhang1Yong Jiang2Albert W. Schulthess3Yusheng Zhao4Jochen C. Reif5Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466 Stadt Seeland, GermanyLeibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466 Stadt Seeland, GermanyLeibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466 Stadt Seeland, GermanyLeibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466 Stadt Seeland, GermanyLeibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466 Stadt Seeland, GermanyCorresponding author.; Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466 Stadt Seeland, GermanyTo extend the contemporary understanding into the grain yield heterosis of wheat, the current study investigated the contribution of deleterious alleles in shaping mid-parent heterosis (MPH). These alleles occur at low frequency in the genome and are often missed by automated genotyping platforms like SNP arrays. The deleterious alleles herein were detected using a quantitative measurement of evolutionary conservation based on the phylogeny of wheat and investigations were made to: (1) assess the benefit of including deleterious alleles into MPH prediction models and (2) understand the genetic underpinnings of deleterious SNPs for grain yield MPH using contrasting crosses viz. elite × elite (Exp. 1) and elite × plant genetic resources (PGR; Exp. 2). In our study, we found a lower allele frequency of moderately deleterious alleles in elites compared to PGRs. This highlights the role of purifying selection for the development of elite wheat cultivars. It was shown that deleterious alleles are informative for MPH prediction models: modelling their additive-by-additive effects in Exp. 1 and dominance as well as associated digenic epistatic effects in Exp. 2 significantly boosts prediction accuracies of MPH. Furthermore, heterotic- quantitative trait loci’s underlying MPH was investigated and their properties were contrasted in the two crosses. Conclusively, it was proposed that incomplete dominance of deleterious alleles contributes to grain yield heterosis in elite crosses (Exp. 1).http://www.sciencedirect.com/science/article/pii/S221451412200157XHybrid wheatGenomic evolutionary rate profilingDeleterious SNPHeterotic Quantitative trait loci |
| spellingShingle | Abhishek Gogna Jie Zhang Yong Jiang Albert W. Schulthess Yusheng Zhao Jochen C. Reif Filtering for SNPs with high selective constraint augments mid-parent heterosis predictions in wheat (Triticum aestivum L.) Crop Journal Hybrid wheat Genomic evolutionary rate profiling Deleterious SNP Heterotic Quantitative trait loci |
| title | Filtering for SNPs with high selective constraint augments mid-parent heterosis predictions in wheat (Triticum aestivum L.) |
| title_full | Filtering for SNPs with high selective constraint augments mid-parent heterosis predictions in wheat (Triticum aestivum L.) |
| title_fullStr | Filtering for SNPs with high selective constraint augments mid-parent heterosis predictions in wheat (Triticum aestivum L.) |
| title_full_unstemmed | Filtering for SNPs with high selective constraint augments mid-parent heterosis predictions in wheat (Triticum aestivum L.) |
| title_short | Filtering for SNPs with high selective constraint augments mid-parent heterosis predictions in wheat (Triticum aestivum L.) |
| title_sort | filtering for snps with high selective constraint augments mid parent heterosis predictions in wheat triticum aestivum l |
| topic | Hybrid wheat Genomic evolutionary rate profiling Deleterious SNP Heterotic Quantitative trait loci |
| url | http://www.sciencedirect.com/science/article/pii/S221451412200157X |
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