Researchers from Kunming Institute of Zoology, Chinese Academy of Sciences, Yunnan Academy of Agricultural Sciences and other institutions have discovered an important allele (elite variety tag single-allele) of upland rice in a new study. nucleotide polymorphism alleles, ETASs). Related papers were published in the journal Nature Communications on July 5. Researcher Wen Wang, deputy director of the Institute of Zoology, Chinese Academy of Sciences and Fengyi Hu, deputy director of the Institute of Food Crops, Yunnan Academy of Agricultural Sciences, are co-corresponding authors of this paper. Researcher Wang Wen has long been devoted to the study of genetic novelties under natural selection and artificial selection and the evolutionary mechanism of their functional origin. He has published many papers in important academic journals such as Science, Nature, Nature Genetics and so on. Hu Fengyi has been devoted to rice variety breeding and related technology research. In recent years, he has published more than 30 research papers and is a reserve talent for young and middle-aged academic and technical leaders in Yunnan Province.
Crop breeding refers to the process of starting with domestication of wild plants and then further improving local crop varieties and fine varieties. Therefore, in essence, crop breeding is a human-guided evolutionary process. Nature and breeding groups provide raw materials for this evolution, and artificial selection of specific traits is the driving force for evolution. Selecting rare and useful mutant genes is crucial for domestication and improvement of crops. However, some important agronomic trait genes are often not found in wild strains and landraces, but in low frequency in some non-good populations.
Asian cultivated rice (Oryza sativa) is the first human domesticated cereal plant. Asian cultivated rice can be two main types: Japonica and Indica, which are domesticated from wild rice O. rufipogon and O. nivara. The domestication and subsequent localization of these crops resulted in the generation of many local rice seeds, providing a lot of genetic resources for rice breeding. For different purposes, such as high yield, crop quality, biotic and abiotic stress, and agronomic adaptability, breeders have successfully cultivated a large number of excellent varieties carrying appropriate allele combinations.
Generally, breeders identify these agronomic trait-related genes by a traditional method called quantitative trait genetic locus (QTL) / gene mapping. This method promotes the identification of a large number of important rice genes. Despite its outstanding advantages, QTL / gene mapping is a time-consuming and labor-intensive method. It takes years to construct isolated populations, and extensive genotyping and phenotyping are required. Another commonly used method: group association mapping (association mapping) often misses elite alleles. In recent years, some population genomics methods have often identified some common alleles, and missed allelic alleles existing in one or a limited number of excellent varieties. In this new article, the researchers first tried a new method to mine alleles of excellent rice varieties. The researchers conducted in-depth sequencing of six elite varieties and identified single-nucleotide polymorphism alleles (ETASs) based on genomic data. Through this preliminary analysis, the researchers identified an ETAS and its characteristics in the gene of the NERAT (9-cis-epoxycarotenoid dioxygenase) gene of the IRAT104 upland rice variety. This allele showed a significant frequency difference between upland rice and irrigated rice, and the researchers observed the presence of selective sweep around this allele. Functional analysis showed that this allele in upland rice is associated with significantly increased abscisic acid levels and increased lateral root density.
The new research reveals an important upland rice allele, and provides us with a potential new strategy for mining rare, important agronomic trait genes.
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