Journal
CROP JOURNAL
Volume 8, Issue 2, Pages 227-242Publisher
KEAI PUBLISHING LTD
DOI: 10.1016/j.cj.2019.09.012
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Funding
- National Key Research and Development Program of China [2016YFD0101803]
- Agricultural Science and Technology Innovation Program (ASTIP) of CAAS
- Fundamental Research Funds for Central Non-Profit of Institute of Crop Science, CAAS [1610092016124]
- Bill and Melinda Gates Foundation
- CGIAR Research Program MAIZE
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On the basis of growing environment, maize can largely be classified into temperate and tropical groups, leaving extensive genetic variation and evolutionary signatures in the maize genome. To identify candidate genes governing flowering time and photoperiod sensitivity, selective signature analysis and SNP- and haplotype-based GWAS were performed using 39,350 high-quality SNP markers in temperate and tropical maize groups consisting of 410 inbred lines phenotyped in three representative experiments in different latitudes. Selective signature analysis revealed 106 selective-sweep regions containing 423 candidate genes involved mainly in biological regulation and biosynthesis pathways. Among these genes, 25 overlapped with known genes governing flowering time and photoperiod sensitivity and 37 were also detected by GWAS for days to tassel, anthesis-silk interval, and photoperiod sensitivity measured by days to silking. Only two of the candidate genes governing flowering time overlapped selective signals. Most haplotype alleles within significant haplotype loci showed the same direction of effect on flowering time and photoperiod sensitivity. The inbred lines carrying GATT at HapL499 (haplotype locus 499) on chromosome 1 had relatively short flowering times. Lines carrying CA at HapL4054 on chromosome 10, TA at HapL4055 on chromosome 10, and GTTGT at HapL978 on chromosome 2 were less sensitive to photoperiod than lines carrying other haplotype alleles. Haplotype loci associated with flowering time and photoperiod sensitivity explained respectively 17.5%-18.6% and 11.2%-15.5% of phenotypic variation. Candidate genes and favorable haplotypes identified in this study may support the more efficient utilization of maize germplasm groups. (c) 2019 Crop Science Society of China and Institute of Crop Science, CAAS. Production and hosting by Elsevier B.V. on behalf of KeAi Communications Co., Ltd. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).
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