Construction Of High-density Recombination Maps Andgenetic Dissection For Drought Tolerance In Maize

Maize is one of the most important food crops and feed source in the world, and a model crop for the study of genetics, evolution and domestication. Maize germplasm is the material base for developing a new variety with high quality, high yield, disease resistance and abiotic stress tolerance. Dissecting excellent alleles of abundant maize germplasm would be useful to improve the breeding efficiency. In this study, a new tempreture nested association mapping(CN-NAM) population was derived from crosses of a common parent Huangzaosi with 11 diverse elite Chinese maize inbred lines, yielding 11 recombination inbred line(RIL) populations and two thousands RILs. Together with previous US-NAM population introduced and included 25 RIL populations and 5000 RILs, the two NAM populations consisted of the research material of this study. On the basis of the NAM populations, high-density markers obtained by Genotyping-By-Sequencing(GBS) were used to construct high-density recombination bin maps and analyze the genomic features of the two NAM populatoions. Additionally, the two NAM populations were phenotyped for drought tolerance related traits under well-watered(WW) and water-stressed(WS) conditions. The genetic architecture of drought tolerance and candidate genes were analyzed by GWAS and joint linkage mapping, coupled with RNA-sequencing of the common parents of the two NAM populations. The main results were as follows: 1. Construction and application of high-density recombination maps in maizeGenetic maps provide the bases for QTL mapping, genetic and evolutionary analysis. High-density markers obtained by GBS were used to construct recombination bin maps. The genetic maps constructed by using each bin as a new marker suggested that the number of markers of genetic map ranged from 734 bins to 2183 bins among individual RIL population, 4932 bins in CN-NAM and 5296 bins in US-NAM, and 6238 bins in CN-US NAM. The results of QTL mapping for days to tasseling(DT) in NAM suggested that recombination maps had the high quality and accuracy, and about 25% DT QTL were overlapped with known flowering-time genes in maize. Compared with the joint linkage mapping results of days to anthesis and days to silking by using medium-density markers map in US-NAM, we found that the high-density markers map could not improve the power of QTL detection, but the resolution of QTL mapping could be increased 50% by using high-density markers map. When conducting joint QTL mapping by combing CN-NAM and US-NAM, the power and resolution of QTL detection could be improved about 50% with the comparison of single NAM mapping.2. Analysis of genomic features in maize nested association mapping populationGenomic features analysis would be useful to understand genetic diversity and phenotypic variation in maize. Genomic features of the two NAM populations were reseachered by high-density recombination maps. The genomic features analysis of two NAMs showed that less segregation distortion and fitness epistasis were widespread in NAM population. The number of recombination events within individual RIL population showed a typical normal distribution. When conducting QTL mapping by using the number of recombination events as a phenotype, a total of 14 QTL were detected in nine RIL populations. Phenotypic variation explained by individual QTL ranged from 5.4% to 17.3%. Segregation distortion analysis within individual RIL population suggested that a total of 445 segregation distortion regions could be found within 36 RIL populations, and 15 common segregation distortion regions could be detected in at least ten RIL populations. About 80% of the known maize gametophytic factors genes controlling segregation distortion were overlapped with highly significant segregation distortion regions. Additionally, we found that the regions with high recombination rate and high gene density usually tended to have less segregation distortion. 3. Genetic architecture of drought tolerance related traits under WW and WSDrought is one of the most important abiotic stress factors limiting maize production. Drought tolerance related traits of the two NAM populations were evaluated under WW and WS, including ASI, plant height(PH), grain yield per plant(GYPP), ear weight(EW), ear length(EL), kernel number per row(KNPR) and hundred kernels weight(HKW). Phenotypic analysis of two NAMs showed that seven drought tolerance related traits had significant difference under WW and WS. In WW and WS, ASI of CN-NAM and US-NAM had significantly negative correlation with the other traits except for EL in WS of CN-NAM and PH in WS of US-NAM. A total of 108 QTL and 91 QTL for seven traits could be detected under WW and WS in CN-NAM, respectively. A total of 112 QTL and 91 QTL for seven traits could be detected under WW and WS in US-NAM, respectively. A total of 32 WW QTL and 18 WS QTL could be found between CN-NAM and US-NAM. Pleitropy analysis among traits showed that no common pleitropy was detected between CN-NAM and US-NAM under WW; pleitropy within CN-NAM and US-NAM was observed between EL and EW, and between HKW and KNPR under WS. A total of 127 and 128 strong associated SNPs for seven traits were separately detected under WW and WS by GWAS in CN-NAM, likely, 95 WW and 51 WS strong associated SNPs in US-NAM. 354 candidate genes were predicted by bioinformatics analysis. 19 candidate gene related with drought tolerance were validated by significantly differential expressed genes under WW and WS obtained by RNA-seq of Huangzaosi and B73.