Comparative population genomic analysis provides insights into breeding of modern indica rice in China
| Autor: | Chao Qin, Milton Brian Traw, Yanchun Zhang, Long Wang, Jianzhuang Wu, Yanru Guo |
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| Rok vydání: | 2021 |
| Předmět: |
Crops
Agricultural Gene Flow 0301 basic medicine China Population Introgression Breeding Subspecies complex mixtures Japonica Evolution Molecular 03 medical and health sciences 0302 clinical medicine parasitic diseases Botany Genetics Cultivar Domestication education Alleles education.field_of_study Oryza sativa biology fungi Haplotype food and beverages Agriculture Oryza General Medicine biology.organism_classification Biological Evolution 030104 developmental biology Haplotypes 030220 oncology & carcinogenesis Edible Grain Genome Plant |
| Zdroj: | Gene. 768:145303 |
| ISSN: | 0378-1119 |
| DOI: | 10.1016/j.gene.2020.145303 |
| Popis: | Comparative genomic analysis within Asian cultivated rice (Oryza sativa L.) populations has greatly enriched our knowledge regarding rice domestication and the divergence of the indica and japonica subspecies, while study on genomic regions associated with improvement within the indica subspecies is still limited. Here, through combined investigation of 2,429 indica cultivar genomes from public sequencing projects, we depict the improvement of modern indica rice in China. We identify three subgroups within indica populations: two geographically distinct, historical subgroups indica I (Ind_I) and indica III (Ind_III) and a modern subgroup indica II (Ind_II). The modern indica subgroup Ind_II shows admixture of the other two subgroups and enrichment of alleles that had been low-frequency in the other two subgroups. The Chinese indica cultivars exhibit a strong subgroup component change from Ind_I to Ind_II in the 1980s. Through haplotype-based comparative analysis, we detect 187 regions associated with separation of Ind_II compared to Ind_I or Ind_III. Within those regions we find strong representation of beneficial agricultural production-related alleles in Ind_II and a positive correlation between grain yield and number of differentiated haplotypes. Phenotypic features of long and slender grain, small tiller angle and decreased flowering time were detected for Ind_II. Through haplotype-based comparative analysis between rice subpopulations and subspecies, we find differentiated haplotypes not only from indica itself but also from japonica and aus, suggesting that introgression from other rice sub-populations has substantially contributed to modern indica rice breeds. These results help clarify the evolutionary landscape of modern indica rice in China and provide useful targets for future improvement. |
| Databáze: | OpenAIRE |
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