Fine Mapping QTLs Associated With Rice Root Traits Of Super Rice Xieyou9308

Rice is one of the major food sources in the world; roots play multiple roles in anchorage of the whole plant, absorbing soil moisture and nutrient, synthetic transportation of amino acids, plant hormones and other bioactive substances during course of the growth and development of plant, and indirectly determined the grain yields, grain quality and lodging resistance et al. Therefore, it is necessary to understand the inheritance of rice root traits, and it is possible to make root studies benefit to rice super high yield breeding. Identification of rice root traits key genes is important for understanding the development of root, and it is great important for creating new rice ideotype. In this study, chromosome segment substitution lines (CSSLs) derived from a cross between R9308(the recurrent parent) and XB (the donor parent) of Xieyou9308, QTLs of plant height, root length, dry weight of root and dry weight of shoots were investigated at heading stage, identification and fine mapping QTLs of root length, root superficial area, root diameter, root volume and number of root tips. The main results were as follows.1. A novel population consisted of sixty eight chromosome segment substitution lines (CSSLs) were developed from advanced backcrosses between R9308(the recurrent parent) and XB (the donor parent) of a super hybrid rice Xieyou9308by molecular marker-assisted selection (MAS). Fourteen strains of CSSLs were selected in BC3F2, and the other fifty four were selected in BC4F2. There were redundant forty nine segments among sixty eight CSSLs except for these target segments, each line carried0-3redundant segments. Twenty eight strains were single segment substitution lines and carried no redundant segments; one redundant segment was carried in each line of these thirty lines, two redundant segment were carried in each line of these nine lines, and three redundant segment were carried in one line, each line carried an average of0.72segments. The CSSLs totally represented the whole genome of nipponbare except for RM3278and Inde151on chromosome3and some deletion in both end of every chromosome, the whole length of substitution segments was more than90%to the whole genome of nipponbare. There were a lot of messages of allelic variations in these CSSLs, and it will play an important role in the study of functional genomics and molecular breeding in rice.2. A total of150BC1F1lines were developed from a cross between R9308and RILs (derived from single-seed-descent method), application of floating culture methods on natural waters to investigate QTLs associated with plant height, root length, dry weight of root and dry weight of shoots of rice in heading stage. A whole of nine QTLs of four traits were detected, they were distributed on chromosome6,7,8,10and11. Three QTLs associated with plant height, two QTLs for root length, dry weight of root and dry weight respectively, and each QTL could explain phenotypic variation was7.92%to21.49%. One major QTL was detected for root length and explained18.14%of the root length phenotypic variation, designated as qRL7. Comparative analysis the QTLs mapping result in early, qRL7was selected for further study.3. Two BC3F2lines in which recombination had occurred within the region containing the target QTL were selected to fine mapping the major QTL of qRL7. There were358recessive individuals in these two populations, nine Indel markers which showed a polymorphism between XB and R9308when assayed by gel electrophoresis were used to fine mapping qRL7. The qRL7was finally mapped to a657.35kb region between markers InDel11and InDel17, The Rice Annotation Project RAP3database (http://rapdb.dna.affrc.go.jp/) predicts96genes in the candidate region for qRL7. It is difficult to predict the candidate gene for qRL7, because of candidate gene was too many.4. Many BC3F3lines in which recombination had occurred within the region containing the target QTLs were selected and application of floating culture methods on natural waters to identify and fine mapping QTLs associated with these root traits. The major QTL-qRSA7associated with root superficial area was located between markers InDell-15and InDell-27, the candidate genomic region of qRSA7spans1578.4kb in the Nipponbare genome, and candidate genes were more than one hundred. The major QTL-qRD7of root diameter was mapped between markers InDel2-13and InDel2-25, there were twenty five genes in this region. The major QTL-qRV8associated with root volume was located between markers InDel3-11and InDel3-20on chromosome8, the candidate genomic region of qRV8spans a large region in the Nipponbare genome, and candidate genes were more than one hundred. The major QTL of qRT7associated with number of root tips was located between markers InDel4-17and InDe14-29, the physical distance between these two markers was972.1kb, the candidate genes was more than one hundred.5. A RILs population (174lines) was developed from a cross between R9308and XB, the parents and F1were planted in Zhejing Fuyang and Hainan Lingshui in rice-growing season of2011, phenotype of heading date at the two environments with molecular genetic linkage map, used winQTL Cart3.0software, was developed for mapping and analyzing the QTLs. A total of12QTL significantly affect heading date were located in chromosome1,2,4,5,6,7, 8and10, the detected QTL individually accounted for4.25%-15.12%of the phenotypic variation. qHD7-1relatively stable expression, had been detected at two environments of trials in Fuyang and Lingshui, accounted for the phenotypic variation ranged from15.12%to13.31%, which positive allele came from the parent of XB.6. Comparative analysis the QTLs mapping results from RILs in early, eight BC3F2lines in which recombination had occurred within the region containing the target QTL with marker assisted selection (MAS) were selected to identify and fine mapping the major QTL of qHD7-1. The qHD7-1was finally mapped to a418kb region between markers InDe123and InDe143, The Rice Annotation Project RAP3database (http://rapdb.dna.affrc.go.jp/) predicts61genes in the candidate region for qHD7-1. It is difficult to predict the accurate candidate gene for qHD7-1, because morphological properties and physiological characteristics of qHD7-1were not understood well. The next work was to narrow the qHD7-1candidate region by using CSSLs until to find this gene, and transgenic function confirmation should be investigated.