Genome-wide Association Studies of Seed Germination Related Traits in Maize

Tian, Runmiao; Zhang, Xue-Hai; Tang, Jihua; Bai, Guanghong; Fu, Zhiyuan

doi:10.3724/sp.j.1006.2018.00672

Cited by 2 publications

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“…For example, the major QTL in Bin 1.09 of umc2047–bnlg1597 region was associated with MESL, COLL, and MESL + COLL, which individually explained 2.89–14.12% of PVE at a single sowing environment ( Table S1 ). Its vicinity, i.e., umc1085–umc1968 region, a QTL for RAT and SDL at 10 cm and 20 cm environments, was identified, which explained 7.19–7.27% of PVE [ 18 ]; near chr01.2532.5 marker, a QTL for germination rate at 12.5 cm sowing depth, was also detected, which explained 3.32% of PVE [ 20 ]; the PZE-101226516–PZE-101229026 region mapped a QTL for seed vigor index, and near PZE-101221874 marker, and a QTL for germination index was found [ 42 ]; and in a genome-wide association study (GWAS), a QTL for seed imbibition volume was identified near the Chr.S_262721257 marker [ 43 ]. These results all indicated that a pleiotropic QTL in the Bin 1.09 region may be a key locus regulating seed vigor, germination ability, and seedling establishment under deep-sowing stress in maize, which could thus be a target in a breeding scheme.…”

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confidence: 99%

Integrated QTL Mapping, Meta-Analysis, and RNA-Sequencing Reveal Candidate Genes for Maize Deep-Sowing Tolerance

Zhao

Niu

Hossain

et al. 2023

IJMS

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Synergetic elongation of mesocotyl and coleoptile are crucial in governing maize seedlings emergence, especially for the maize sown in deep soil. Studying the genomic regions controlling maize deep-sowing tolerance would aid the development of new varieties that are resistant to harsh conditions, such as drought and low temperature during seed germination. Using 346 F2:3 maize population families from W64A × K12 cross at three sowing depths, we identified 33 quantitative trait loci (QTLs) for the emergence rate, mesocotyl, coleoptile, and seedling lengths via composite interval mapping (CIM). These loci explained 2.89% to 14.17% of phenotypic variation in a single environment, while 12 of 13 major QTLs were identified at two or more sowing environments. Among those, four major QTLs in Bin 1.09, Bin 4.08, Bin 6.01, and Bin 7.02 supported pleiotropy for multiple deep-sowing tolerant traits. Meta-analysis identified 17 meta-QTLs (MQTLs) based on 130 original QTLs from present and previous studies. RNA-Sequencing of mesocotyl and coleoptile in both parents (W64A and K12) at 3 cm and 20 cm sowing environments identified 50 candidate genes expressed differentially in all major QTLs and MQTLs regions: six involved in the circadian clock, 27 associated with phytohormones biosynthesis and signal transduction, seven controlled lignin biosynthesis, five regulated cell wall organization formation and stabilization, three were responsible for sucrose and starch metabolism, and two in the antioxidant enzyme system. These genes with highly interconnected networks may form a complex molecular mechanism of maize deep-sowing tolerance. Findings of this study will facilitate the construction of molecular modules for deep-sowing tolerance in maize. The major QTLs and MQTLs identified could be used in marker-assisted breeding to develop elite maize varieties.

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