Genomic regions and candidate genes selected during the breeding of rice in Vietnam
Abstract Vietnam harnesses a rich diversity of rice landraces adapted to a range of conditions, which constitute a largely untapped source of diversity for the continuous improvement of cultivars. We previously identified a strong population structure in Vietnamese rice, which is captured in five In...
| Main Authors: | , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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Wiley
2022-07-01
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| Series: | Evolutionary Applications |
| Subjects: | |
| Online Access: | https://doi.org/10.1111/eva.13433 |
| _version_ | 1818471473764892672 |
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| author | Janet Higgins Bruno Santos Tran Dang Khanh Khuat Huu Trung Tran Duy Duong Nguyen Thi Phuong Doai Anthony Hall Sarah Dyer Le Huy Ham Mario Caccamo Jose DeVega |
| author_facet | Janet Higgins Bruno Santos Tran Dang Khanh Khuat Huu Trung Tran Duy Duong Nguyen Thi Phuong Doai Anthony Hall Sarah Dyer Le Huy Ham Mario Caccamo Jose DeVega |
| author_sort | Janet Higgins |
| collection | DOAJ |
| description | Abstract Vietnam harnesses a rich diversity of rice landraces adapted to a range of conditions, which constitute a largely untapped source of diversity for the continuous improvement of cultivars. We previously identified a strong population structure in Vietnamese rice, which is captured in five Indica and four Japonica subpopulations, including an outlying Indica‐5 group. Here, we leveraged that strong differentiation and 672 native rice genomes to identify genomic regions and genes putatively selected during the breeding of rice in Vietnam. We identified significant distorted patterns in allele frequency (XP‐CLR) and population differentiation scores (FST) resulting from differential selective pressures between native subpopulations, and later annotated them with QTLs previously identified by GWAS in the same panel. We particularly focussed on the outlying Indica‐5 subpopulation because of its likely novelty and differential evolution, where we annotated 52 selected regions, which represented 8.1% of the rice genome. We annotated the 4576 genes in these regions and selected 65 candidate genes as promising breeding targets, several of which harboured alleles with nonsynonymous substitutions. Our results highlight genomic differences between traditional Vietnamese landraces, which are likely the product of adaption to multiple environmental conditions and regional culinary preferences in a very diverse country. We also verified the applicability of this genome scanning approach to identify potential regions harbouring novel loci and alleles to breed a new generation of sustainable and resilient rice. |
| first_indexed | 2024-04-14T03:50:48Z |
| format | Article |
| id | doaj.art-976852a9aba5465fa8e39952586c2d32 |
| institution | Directory Open Access Journal |
| issn | 1752-4571 |
| language | English |
| last_indexed | 2024-04-14T03:50:48Z |
| publishDate | 2022-07-01 |
| publisher | Wiley |
| record_format | Article |
| series | Evolutionary Applications |
| spelling | doaj.art-976852a9aba5465fa8e39952586c2d322022-12-22T02:14:01ZengWileyEvolutionary Applications1752-45712022-07-011571141116110.1111/eva.13433Genomic regions and candidate genes selected during the breeding of rice in VietnamJanet Higgins0Bruno Santos1Tran Dang Khanh2Khuat Huu Trung3Tran Duy Duong4Nguyen Thi Phuong Doai5Anthony Hall6Sarah Dyer7Le Huy Ham8Mario Caccamo9Jose DeVega10Earlham Institute Norwich UKNIAB Cambridge UKAgriculture Genetics Institute (AGI) Hanoi VietnamAgriculture Genetics Institute (AGI) Hanoi VietnamAgriculture Genetics Institute (AGI) Hanoi VietnamAgriculture Genetics Institute (AGI) Hanoi VietnamEarlham Institute Norwich UKNIAB Cambridge UKAgriculture Genetics Institute (AGI) Hanoi VietnamNIAB Cambridge UKEarlham Institute Norwich UKAbstract Vietnam harnesses a rich diversity of rice landraces adapted to a range of conditions, which constitute a largely untapped source of diversity for the continuous improvement of cultivars. We previously identified a strong population structure in Vietnamese rice, which is captured in five Indica and four Japonica subpopulations, including an outlying Indica‐5 group. Here, we leveraged that strong differentiation and 672 native rice genomes to identify genomic regions and genes putatively selected during the breeding of rice in Vietnam. We identified significant distorted patterns in allele frequency (XP‐CLR) and population differentiation scores (FST) resulting from differential selective pressures between native subpopulations, and later annotated them with QTLs previously identified by GWAS in the same panel. We particularly focussed on the outlying Indica‐5 subpopulation because of its likely novelty and differential evolution, where we annotated 52 selected regions, which represented 8.1% of the rice genome. We annotated the 4576 genes in these regions and selected 65 candidate genes as promising breeding targets, several of which harboured alleles with nonsynonymous substitutions. Our results highlight genomic differences between traditional Vietnamese landraces, which are likely the product of adaption to multiple environmental conditions and regional culinary preferences in a very diverse country. We also verified the applicability of this genome scanning approach to identify potential regions harbouring novel loci and alleles to breed a new generation of sustainable and resilient rice.https://doi.org/10.1111/eva.13433allele mininggenome scanlandracesriceselection |
| spellingShingle | Janet Higgins Bruno Santos Tran Dang Khanh Khuat Huu Trung Tran Duy Duong Nguyen Thi Phuong Doai Anthony Hall Sarah Dyer Le Huy Ham Mario Caccamo Jose DeVega Genomic regions and candidate genes selected during the breeding of rice in Vietnam Evolutionary Applications allele mining genome scan landraces rice selection |
| title | Genomic regions and candidate genes selected during the breeding of rice in Vietnam |
| title_full | Genomic regions and candidate genes selected during the breeding of rice in Vietnam |
| title_fullStr | Genomic regions and candidate genes selected during the breeding of rice in Vietnam |
| title_full_unstemmed | Genomic regions and candidate genes selected during the breeding of rice in Vietnam |
| title_short | Genomic regions and candidate genes selected during the breeding of rice in Vietnam |
| title_sort | genomic regions and candidate genes selected during the breeding of rice in vietnam |
| topic | allele mining genome scan landraces rice selection |
| url | https://doi.org/10.1111/eva.13433 |
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