Genome Variation Analysis And QTL Mapping Analysis Of Some Triats In Teosinte

Maize is not only one of the three major grain crops in China, but also the most productive crop in the world, playing an important role in national economy and people’s lives. But in recent years, maize production and breeding faced a series of problems, for example, simplification of promotion cultivars, the genetic basis of breeding material became more and more narrow, gene pool got poor increasingly. Distant hybridization by using teosinte which is maize relatives taxa and maize can improve maize, enlarge the gene pool and the germplasm resources of maize and get many genes about excellent characters, it’s a key of maize breeding in the future. In this experiment, we used genome re-sequencing sequences of teosinte compare with reference genome sequences of B73, mastered the information of SNP and InDel variations in teosinte, and developed InDel markers can apply to routine laboratory, the work laid a foundation for molecular marker assisted breeding. At the same time, we also built a linkage map of maize and teosinte to identify QTL, which provided theoretical basis for importing the excellent genes from teosinte into maize in the future. The main results were as follows:1.The present study performed genome-wide variation analysis of whole genome re-sequencing sequences of teosinte, identified 8,041,081 SNPs and 586,943 InDels in the whole genome, and 1,092,216 SNPs and 141,237 InDels in the coding region. We found the number of A-G, C-T, G-A and T-C were the most in the whole genome or coding region by the statistical of SNP variation types, accounted for 66.86% of the SNP variation in the genome, and 63.14% of the SNP variation in the coding region. Meanwhile,the number of insertions and deletions are the same basically in the InDel variations. Furthermore, we identified 9,445/481 SNP high/low regions and 607/32 InDel high/low regions by the statistical of frequencies of SNPs and InDels at a 100kb sliding window in each chromosome.2. In 586,943 InDels, the number of 1-5 bp InDels is 547,227, accounted for 93.23% of the total, the number of 1-10 bp InDels is 573,505, accounted for 97.71% of the total. The study selected the detected InDels which distributed on the ten chromosomes of maize uniformly to design 141 pairs of InDel primers. and used three maize materials including Mo17,1212 and zheng58 and three teosinte materials including M-1. M-4 and M-6 to polymorphism validation.The result showed that there were 122 pairs of InDel primers can get amplification products, and 106 pairs of InDel primers had differences between mazie and teosinte, accounted for 86.89%.3.In this study. We constructed a 148 F2 populations by using maize inbred line 1212 and teosinte M-1. after the SNP analysis of F2 population, we got a data containing 3,072 SNP markers. Through layers of screening, we selected the better of 419 SNP markers to build a genetic map which the total length of 1404.21cM and average distance of 3.35cM. Among them, the longest linkage map which the total length of 220.03cM and average distance of 4.31 cM is chrl. the shortest linkage map which the total length of 101.95cM and average distance of 2.76cM is chr4.4.Combined the trait data of F2.3 population which from 148 F2 population constructed by using maize inbred line 1212 and teosinte M-1 on plant height to detect QTL, we detected four QTL locis containing qPH-1-1, qPH-1-2, qPH-7, qPH-9 on whole-genome which located on the chrl, chr7 and chr9 respectively. qPH-1-1 and qPH-1-2 are located on chr1. qPH-1-1 is located on between PZE-101168807 and PZE-101166671, and the contribution rate is 9.32%. qPH-1-2 is located on between PZE-101043682 and PZE-101041837, and the contribution rate is 7.58%. qPH-7 is located on between SYN17951 and PUT-163a-71300000-3068, and the contribution rate is 6.08%. qPH-9 is located on between PZE-109047418 and PZE-109038360, and the contribution rate is 12.77%. Combined the trait data of F2:3 population on tiller to detect QTL, we detected two QTL locis containing qPT-1, qPT-2 on the whole-genome which located on chrl and chr2 respectively. qPT-1 is located on between PZE-101041837 and PZE-101035640, and the contribution rate is 8.81%. qPT-2 is located on between PZE-110009618 and SYN17100, and the contribution rate is 8.79%.