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Resequencing of 1,143 indica rice accessions reveals important genetic variations and different heterosis patterns.

ABSTRACT: Obtaining genetic variation information from indica rice hybrid parents and identification of loci associated with heterosis are important for hybrid rice breeding. Here, we resequence 1,143 indica accessions mostly selected from the parents of superior hybrid rice cultivars of China, identify genetic variations, and perform kinship analysis. We find different hybrid rice crossing patterns between 3- and 2-line superior hybrid lines. By calculating frequencies of parental variation differences (FPVDs), a more direct approach for studying rice heterosis, we identify loci that are linked to heterosis, which include 98 in superior 3-line hybrids and 36 in superior 2-line hybrids. As a proof of concept, we find two accessions harboring a deletion in OsNramp5, a previously reported gene functioning in cadmium absorption, which can be used to mitigate rice grain cadmium levels through hybrid breeding. Resource of indica rice genetic variation reported in this study will be valuable to geneticists and breeders.

SUBMITTER: Lv Q

PROVIDER: S-EPMC7508829 | biostudies-literature | 2020 Sep

REPOSITORIES: biostudies-literature

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Resequencing of 1,143 indica rice accessions reveals important genetic variations and different heterosis patterns.

Lv Qiming Q Li Weiguo W Sun Zhizhong Z Ouyang Ning N Jing Xin X He Qiang Q Wu Jun J Zheng Jiakui J Zheng Jiatuan J Tang Shaoqing S Zhu Renshan R Tian Yan Y Duan Meijuan M Tan Yanning Y Yu Dong D Sheng Xiabing X Sun Xuewu X Jia Gaofeng G Gao Hongzhen H Zeng Qin Q Li Yufei Y Tang Li L Xu Qiusheng Q Zhao Bingran B Huang Zhiyuan Z Lu Hongfeng H Li Na N Zhao Jian J Zhu Lihuang L Li Dong D Yuan Longping L Yuan Dingyang D

Nature communications 20200922 1

Obtaining genetic variation information from indica rice hybrid parents and identification of loci associated with heterosis are important for hybrid rice breeding. Here, we resequence 1,143 indica accessions mostly selected from the parents of superior hybrid rice cultivars of China, identify genetic variations, and perform kinship analysis. We find different hybrid rice crossing patterns between 3- and 2-line superior hybrid lines. By calculating frequencies of parental variation differences ( ...[more]

PMID: 32963241

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Project description:BackgroundVietnam possesses a vast diversity of rice landraces due to its geographical situation, latitudinal range, and a variety of ecosystems. This genetic diversity constitutes a highly valuable resource at a time when the highest rice production areas in the low-lying Mekong and Red River Deltas are enduring increasing threats from climate changes, particularly in rainfall and temperature patterns.ResultsWe analysed 672 Vietnamese rice genomes, 616 newly sequenced, that encompass the range of rice varieties grown in the diverse ecosystems found throughout Vietnam. We described four Japonica and five Indica subpopulations within Vietnam likely adapted to the region of origin. We compared the population structure and genetic diversity of these Vietnamese rice genomes to the 3000 genomes of Asian cultivated rice. The named Indica-5 (I5) subpopulation was expanded in Vietnam and contained lowland Indica accessions, which had very low shared ancestry with accessions from any other subpopulation and were previously overlooked as admixtures. We scored phenotypic measurements for nineteen traits and identified 453 unique genotype-phenotype significant associations comprising twenty-one QTLs (quantitative trait loci). The strongest associations were observed for grain size traits, while weaker associations were observed for a range of characteristics, including panicle length, heading date and leaf width.ConclusionsWe showed how the rice diversity within Vietnam relates to the wider Asian rice diversity by using a number of approaches to provide a clear picture of the novel diversity present within Vietnam, mainly around the Indica-5 subpopulation. Our results highlight differences in genome composition and trait associations among traditional Vietnamese rice accessions, which are likely the product of adaption to multiple environmental conditions and regional preferences in a very diverse country. Our results highlighted traits and their associated genomic regions that are a potential source of novel loci and alleles to breed a new generation of low input sustainable and climate resilient rice.

Project description:BackgroundIdentification of the allelopathy-interrelated metabolites from the allelopathic rice rhizosphere is crucial to understand the allelopathic mechanism of rice, which in turn can promote its applications to farming. In this study, the metabolites from the rhizosphere soil of five different rice lines, including allelopathic rice accession PI312777 (PI) and non-allelopathic rice accession Lemont (Le) as well as their genetic derivatives (e.g., phenylalanine ammonia-lyase (PAL) gene overexpression transgenic lines of PI and Le, namely, PO and LO respectively, and PAL RNA interference line of PI, namely, PR) were identified and comparatively analyzed to explore the positive compounds that are involved in the process of rice allelopathy.ResultsThe results showed that 21 non-polar compounds and 21 polar compounds differed in content in the rhizosphere soil of PI and Le, which include several volatile fatty acids and long-chain fatty acids. The relative contents of fatty acids also differed between PAL overexpressing or RNA interference (RNAi)-silenced line and their wild-type respectively. Acetic acid content also differed among groups, i.e., it is higher in the high allelopathic potential rice. Further analysis showed that different metabolites from the ADS8 resin-extracted phase were more abundant than that those from the ADS21 resin-extracted phase, suggesting that the allelochemicals in root exudates of allelopathic rice are mainly non-polar substances. KEGG annotation of these differential metabolites revealed that these compounds were related to nutrient metabolism, secondary metabolite synthesis, signaling substance synthesis, and toxin degradation.ConclusionsRice allelochemicals deposited in the ADS8 resin-extracted phase were more abundant than those in the ADS21 resin-extracted phase. Allelochemicals in root exudates of allelopathic rice are mainly non-polar substances, and long-chain fatty acids are considered as allelopathy interrelated metabolites.

Dataset Information

Resequencing of 1,143 indica rice accessions reveals important genetic variations and different heterosis patterns.

Publications

Resequencing of 1,143 indica rice accessions reveals important genetic variations and different heterosis patterns.

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