The new method can quickly locate and clone the quantitative traits of rice

The new method can quickly locate and clone the quantitative traits of rice

The new method can quickly locate and clone the quantitative trait locus of rice.

Photo courtesy of Huazhong Agricultural University, a parent combination of F2 gradient populations of grain length and grain width

 Photo courtesy of Huazhong Agricultural University, a parent combination of F2 gradient populations of grain length and grain width

Recently, "Nature-Communication" published online the latest research papers of the rice team of the State Key Laboratory of Crop Genetic Improvement of Huazhong Agricultural University and the research group of Professor Li Yibo from Hubei Hongshan Laboratory
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The research developed a new method for rapid and high-throughput cloning of quantitative trait locus (QTL) genes—RapMap, and discovered the essential criteria for unit-site inheritance, and quickly cloned 8 rice seed size QTL genes, and revealed The slender shape of indica rice is the result of directional selection in the process of long-term domestication and improvement of rice

The yield, quality, and traits related to biotic and abiotic stress of crops are mostly controlled by quantitative trait loci.
Genetic analysis and molecular cloning of these quantitative trait loci are the basis for understanding genetic diversity and genetically improved crops
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Obtaining a genetic mapping population separated by a single point is a prerequisite for cloning QTL genes

In order to improve the efficiency of obtaining a single-site genetic population, the study first summarized 12 unit-site genetic segregation models based on the three genetic effects of dominant, semi-dominant, and super-dominant, and proposed a single-site genetic segregation model on this basis.
The essential feature is that the two homozygous genotypes of the target QTL/gene segment in any genetic segregation population can co-segregate with the corresponding phenotype, that is, the co-segregation criterion
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This "co-segregation criterion" is a necessary and sufficient condition for unit point inheritance, which corrects and clarifies the traditional judgment criteria of unit point genetic segregation in genetics (such as bimodal distribution, 3:1 segregation ratio, etc.

In order to meet the co-segregation criteria of segregating populations as much as possible, the study proposed and practiced a strategy of selecting parents with small phenotypic differences from the core collection to construct a series of F2 gradient populations for genetic mapping, in order to minimize each genetic population.
Control the number of separation sites for the target trait, and clone the major QTLs in different parent combinations
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Groups that do not meet the co-segregation criteria can be self-bred in several families with low, medium, and high values ​​of F2 or F3.

The F2 gradient population combined with the co-segregation standard of unit site genetics realizes the "trinity" gene location and cloning strategy of QTL mapping, verification and similar gene line screening, which greatly saves the time and cost of obtaining a unit site genetic location population
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In this study, by constructing 15 seed size F2 gradient populations, 8 seed size genes were cloned within three years, including two new genes GL1 and GW5.

Compared with traditional mapping populations and positioning methods, RapMap's advantages are mainly manifested in: RapMap has both the accuracy of parental genetic populations and the genetic diversity of multiple parental genetic populations; F2 gradient populations realize the simplicity of parental selection and population construction , Flexibility and comprehensiveness, short construction time and low cost; RapMap uses co-segregation standards to achieve the "trinity" of the three key links of QTL cloning, QTL mapping, QTL effect verification, and similar gene line screening, which greatly improves QTL The accuracy and efficiency of cloning are based on gene cloning as a target-oriented method; RapMap can not only clone major genes in natural mutations, but also identify and clone rare mutations and minor genes in natural populations; RapMap does not rely on complex Based on the direct correspondence between genotype and phenotype, it avoids the interference of false positives and false negatives, and improves the reliability of QTL mapping and cloning; through the F2 gradient population combined with the co-separation standard, RapMap can effectively Reduce complex polygene inheritance to simple unit point inheritance, so as to realize the breakthrough of cloning only one major QTL gene for one population and cloning multiple QTL genes in batches for multiple populations
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The above characteristics show that the RapMap method, with the construction of gradient genetic populations and the "co-segregation standard" of unit site inheritance as the core, is a rapid and high-throughput "triad" that integrates QTL mapping, verification, and screening of similar and near-isogenic lines.
Gene cloning strategy
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This method is also applicable to any traits of plants and animals that are easy to cross and reproduce enough hybrid offspring, or will become the universal and preferred method for QTL gene mapping and cloning, and will help functional genomics and genetics research

The research was funded by the National Key Research and Development Program, the National Natural Science Foundation of China, and the Independent Innovation Fund of Huazhong Agricultural University
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(Source: China Science News Li Chen)

Related paper information: https://doi.

https://doi.
org/10.
1038/s41467-021-25961-1