High-density Linkage Map Construction, Mapping of Agronomic Traits in Tropical Maize (Zea Mays L.) and Validating SNPs Controlling Maize Grain Yield and Plant Height in Southern Hybrid Testcrosses
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Texas, as the major maize producer in the Southern United States, faces serious problems in maize production (i.e. drought stress and aflatoxin contamination) as well as in maize breeding. In the Texas A&M maize breeding program, a previous genome- wide association study was conducted using a diverse panel of 346 inbred lines testcrossed to Tx714, and three quantitative trait variants (QTV1, QTV2 and QTV3) were identified, explaining 3-5% variation of grain yield under irrigated and non-irrigated conditions. In this present study, we constructed three bi-parental linkage populations (Ki3/NC356, Tx740/NC356 and LH82/LAMA-YC) and tested these as lines per se and as hybrid test crosses to validate three QTVs’ effects and map QTLs for multiple agronomic traits using high-density SNP array. The alleles at QTV1 and QTV3 from inbred line NC356 were detected significantly increasing plant height, flag leaf height and grain test weight in the Ki3/NC356 population across all tests over two years; QTV2 was identified significant with minor effects on flowering time in Ki3/NC356 F3:4 progenies. In the other two populations, few consistent and significant QTVs’ effects were validated, accounting for the limited population size and substantial field variation in our experimental environments. Three high-density linkage maps were developed, with the average interval distance at 1.0cM. For the Ki3/NC356 population, a total of eighteen QTLs were detected for all traits using BLUEs; twenty-two QTLs were detected when using BLUPs. There were eight QTLs confirmed consistent by both BLUPs, and BLUEs and fourteen candidate genes were implicated. For the Tx740/NC356 population, twenty-five QTLs were detected using BLUEs and five consistent QTLs were identified by both BLUPs and BLUEs; six candidate genes were predicted. For the LH82/LAMA-YC population, only seven QTLs were mapped using BLUEs and one QTL was detected using BLUPs. In this study, three bi-parental linkage populations were derived from tropical maize germplasm, which are adaptive to Texas environments and also good resources for Texas maize breeding. The QTLs identified in this study were promising candidates for further gene cloning and genic function analysis in future.
Chen, Yuanyuan (2016). High-density Linkage Map Construction, Mapping of Agronomic Traits in Tropical Maize (Zea Mays L.) and Validating SNPs Controlling Maize Grain Yield and Plant Height in Southern Hybrid Testcrosses. Doctoral dissertation, Texas A & M University. Available electronically from