Genome-wide Association Functional Studies (GWAFS) of Candidate Genes for Germination-related Traits of Low Temperature Tolerance in Maize (Zea mays L.)

Lin Heying¹, Ren Zhiqiang^{1, 2,} , Hafeez Noor^{1, 3} and Waseem Bashir³

¹Shanxi Agricultural University, Taiyuan 030006, Shanxi, China

²Shanxi Institute of Organic Dryland Farming, State Key Laboratory of Sustainable Dryland Agriculture (in preparation), Shanxi Key Laboratory of Organic Dry Farming,Shanxi Agricultural University, Shanxi, 030031;Key Research and Development Program of Shanxi province (202102140601002-1)

³Lasbela University of Agriculture, Water & Marine Sciences (LUAWMS)Balochistan, Pakistan

Cite this paper:
Lin Heying, Ren Zhiqiang, Hafeez Noor and Waseem Bashir. Genome-wide Association Functional Studies (GWAFS) of Candidate Genes for Germination-related Traits of Low Temperature Tolerance in Maize (Zea mays L.). Journal of Food and Nutrition Research. 2024; 12(5):318-326. doi: 10.12691/jfnr-12-5-11

Abstract

Different maize inbred lines display various low-temperature resistance, but the dynamic changes in seed germination under low-temperature stress in maize remain unknown, especially at the transcriptome level. Maize (Zea mays L.) originated in tropical and subtropical areas and is naturally sensitive to low-temperature stress, especially during seed germination. As spring maize, seed germination and seedling growth at an early stage are usually subjected to low-temperature stress. In this study, 18 evaluation indexes of low temperature tolerance germination of 238 maize inbred lines were statistically analyzed, of which 12 evaluation indexes of low temperature tolerance had large coefficient of variation. The results of cluster analysis relative decrease of root length is similar to those of comprehensive evaluation cluster analysis of 12 low temperature tolerance indexes. The relative decrease of root length ranges from 0.105 to 0.936, which conforms to the normal distribution and can distinguish the tolerance of low-temperature germination, the K + Q model was used to set the threshold - log10P = 4.61 to score the GWAS of evaluation indexes of low temperature tolerance. A total of 47 SNP loci significantly associated with low temperature tolerance were detected, of which the SNP loci significantly associated with chromosome 8 were the most, and the interpretation range of phenotypic contribution rate was 10.88% - 16.31%. The results of F_2:3 population linkage analysis were consistent with the gene candidate region predicted by GWAS. BSA-seq analysis showed that there were 13 all indexes on chromosome 3 between 220.9 Mb and 221.3 Mb. The average value of all index in the extreme mixed pool of the two offspring was -0.089. Therefore, the candidate interval of this study is located on chromosome 3 220.9 Mb-221.3 Mb. There are 21 candidate genes in the localization interval.

Keywords:
seed germination seedling growth low-temperature stress maize peroxidase activity

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