Development Of Genetic Markers And Germplasm Associated Wtih Straighthead Resistance Through Fine Mapping In Rice

Rice（oryza sativa L.）, is one of the most important food crops in the world. In Asia where has the largest population around the world, most pepole live here are feeded by rice, in this case, rice production security is important component of world food security. Rice growing in USA originated in South of Carolina state in1690. First rice produce record was in1895, at that time there was hundreds of thousands of hectares rice planting area. Then rice growing area kept increasing. Until now, it maintains in about1.2million hectares in USA. Rice produce area is distributed in California in west coast, and several states in Southern USA. Most of the varieties grown in USA are japonica, and according to USA market standard they were classified into three groups, including:long-grain rice, medium-grain rice and short-grain rice. The total rice production of USA is not very high, but most of rice produced here is for exportation, which made the USA as the world’s second largest exporter, therefore, rice production security in USA is one of the important part of world food security. The major rice diseases happened in USA inculding:sheath blight, blast, sclerotinia, the leaf sheaths black rot, rice brown spot disease, kernel smut, blight and straighthead.Straighthead, a physiological disorder characterized by sterile florets and distorted spikelets, causes significant yield losses in rice, and occurs in many countries. Straighthead happens frequently in southen USA where about90%of USA rice is produced, however, most of rice varieties grown here are susceptible to straighthead. In this case, straighthead is a huge threat for rice production in USA and worldwide. The current control method of draining paddies early in the season stresses plants, is costly, and wastes water. Development of resistant cultivar is regarded as the most efficient way for its control. However, because of uncertain of straighthead causal factor and lacking of resistant germplasm, a little progress was made in resistant breeding until2000. Although a lot of factors were reported to involved in straighthead disorder by previous studies, arsenic is considered as the most important one. Straighthead is very difficult to be directly evaluated, because instability of heritance of nature straighthead. Since the1980s, the breeding community has used soil incorporation of As in the form of MSMA as a common practice for evaluating rice susceptibility to straighthead. In this study, two recombinant inbred line （RIL） F9populations were developed for linkage mapping and fine mapping of straighthead resistance gene. Result showed that:1) Two RIL F9populations were phenotyped over two years using monosodium methanearsonate （MSMA） to induce the symptoms. One population of170RILs was genotyped with136SSRs, polymorphsm frequency is26.1%, the other population of91RILs was genotyped with159SSRs, polymorphsm frequency is37.2%.2) We fine mapped a gene for straighthead resistance by linkage mapping and fine mapping. A major QTL qSH-8was identified in an overlapping region in both populations, and explained46%of total variation in one and67%in another population for straighthead resistance. qSH-8was fine mapped from1.0Mbp to340kb using7SSR markers and further mapped to290kb in a population between RM22573and InDel27using4InDel markers. A total of36putative genes were detected in this region.3) According to the information from Gramene data base, a total of36putative genes were found in the fine mapped region. According to the information from Geneinvestigator data base, protein expression level of the36putative genes at different rice growning stage was investigated. The result showed that:3putative genes, LOC₀8g10240.10340and10380, their protein expression level were detected to decrease significantly.4) Two molecular markers, SSR AP3858-1and InDel11, were within the fine mapped region, and co-segregated with straighthead resistance in both RIL populations. Then we constructed a world germplasm collection which contian72accessions selected from USDA core collection for marker verification. These accessions were selected based on their representation of global diversity and diverse straighthead responses. The χ2test result showed that P value of two markers, InDel11and AP3858-1, were0.0014and0.0004, respectively; in InDel11,78%of the genotypes matching the phenotypes among those global accessions, and in AP3858-1was76%. These results demonstrated that AP3858-1and InDel11significantly associated with straighthead resistance and can be used for marker-assisted selection （MAS） for straighthead resistant cultivars, which is especially important because there is no effective way to directly evaluate straighthead resistance.5) Five straighthead resistance RILs from Cocodire/Jing185F9population, RIL369,397,404,407、469and506, which showed genotype of resistant parent at AP3858-1and InDel11loci. Furthermore, they were found to have more than50%of similarity with Cocodrie, moreover, some of their agronomic traits showed no significant differnce from Cocodrie or even better. In this case, these RILs can be used to improve straighthead resistance for susceptible varieties in southern USA.