Analysis Of Genetic Diversity And Haplotype Of Rht2Gene And Its Flanking Sequence In Wheat

In the1960s and the1970s,"green revolution" makes a substantial increase in crop yields around the world. Rht-Dlb (Rht2), one of the wheat "green revolution" genes, originated from mutation of Rht-Dl which regulated plant response to gibberellin signal and was located in wheat4D short arm of chromosome. To analyze the diversity change of Rht-Dl gene in the process of domestication and breeding, one can not only understand selection and evolution of Rht2gene but also provide a scientific basis for the breeding of the Rht2gene. In this study, the Rht-D1gene and flank region were sequenced and SNPs were detected in45Aegilops tauschii,51landraces and80modern breeding varieties. The result is as follows:1. Rht-D1and its flank51fragments, a total of56Kb in7.5cM in the4D chromosome of wheat, were sequenced for45Aegilops tauschii,51landraces and80modern breeding varieties (including34accession with Rht2).563SNPs were detected in wild material, average about1SNP/100.14bp while14SNPs were detected in wheat cultivars, average about1SNPs/4027bp. It was shown that lost rate of SNPs is as high as98%in the progress of domestication from wild species to landraces, which is much higher than the value previously reported. The nucleotide diversity (0.00300) and Shannon’s information index (Ⅰ)0.579) in wild species are significantly higher than that in cultivars (0.00009,0.524) indicating that there is a serious bottleneck in the process of domestication in this region, resulting in a lack of diversity of the D genome of wheat. It is an effective way to solve the poor genetic diversity in common wheat that synthetic wheat was cultivated using Aegilops tauschi.The study also found that the diversity of ssp. eusquarrosa subspeciesis higher than ssp. strangulala subspecies in Aegilops tauschi.2.1Rht-D1haplotypes(Ⅰ-Ⅶ) were found based on13SNPs detected in wild species and cultivars, five of Which(Ⅰ-Ⅴ)were presented in wild species, while three haplotypes (Ⅴ-Ⅶ) were presented in wheat cultivars. Haplotype V is shared by wild species and wheat cultivars. Evolutionary relatives among7Rht-Dl haplotypes is defined. A new haplotype (HapVll) which can reduce plant height by16%was found in wheat cultivars. Wheat modern breeding varieties Afu, Abo and Zhengyinlhao, elite parent which belong to the haplotype (IX), not only promote the large releasing area, long duration but also make a vital contribution for Chinese even the world wheat. HapVII played an important role in the improvement of the wheat, So it was considered as haplotype of "green revolution". There arc rich types of haplotypes to be developed and utilized in the future in Aegilops tauschii.3. Population structure of131wheat cultivars was investigated using42pairs of SSR distributed in the whole wheat genome. The structure result at K=2was the best separator providing the highest delta k value. That is, the131wheat cultivars were divided into two groups:landraces and modern breeding varieties based42SSR markers. Fst values were calculated using14SNPs detected in7.5cM region containing Rht2for131wheat cultivars. The results shown that there are significant genetic differences between cultivars with Rht2and cultivars without Rht2. Analysis of LD revealed that there is recombination hotspot in5’upstream of Rht-D1gene. The recombination hotspot divided the7.5cM region containing Rht2into two haplotype blocks. In the haplotype block containing Rht2, the diversity order of the Rht-D1gene and three SNPs is modern breeding varieties>landraces, foreign landraces> Chinese landraces. However, in the haplotype block upstream Rht-D1, the diversity order of the Rht-D1gene and four SNPs is landraces> modern breeding varieties, Chinese landraces> foreign landraces.4. Four haplotypes were presented in wheat cultivars with Rht2based on LD. The major haplotypes is Ⅰ and Ⅲ. Norin10and Suwon86which is considered as foreign dwarf sources belong to the haplotype Ⅰ, while Huixianhong and Youbao which is considered as Chinese dwarf sources belong to the haplotype Ⅲ, indicating that the Chinese "green revolution" of wheat is conducted in parallel with the international "green revolution".5. The diversity was analyzed for8genes regulating plant development, stress resistance, storage, transshipment and other important functions in7.5cM except Rht2, respectively.107SNPs were detected in45Aegilops tauschii, average about1SNP/161bp while2SNPs were detected in131wheat cultivars, average about1SNPs/7092bp in14Kp fragment of8genes. It can be concluded that the lost rate of SNPs is as high as98.13%in8genes in the progress of domestication of wheat. Ols gene encoding storage proteins and Ptd gene encoding peptidase have the least number of haplotypes (3and4) in8genes, inferring that this two genes may experience negative selection during the long process of evolution when deleterious haplotypes might be removed from the population. However, Erf and Zcj gene have the most number of haplotypes (10and11) in8genes. Erf and Zcj gene involving in plant growth and development and responsing to environmental stress have a high haplotype diversity to enhance the ability of crops to adapt to the environment.