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

Abstract

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.

Exogenous Serotonin (5-HT) Promotes Mesocotyl and Coleoptile Elongation in Maize Seedlings under Deep-Seeding Stress through Enhancing Auxin Accumulation and Inhibiting Lignin Formation

“…In addition, the deep seeding is not conducive to seedlings' emergence in maize. There was a significantly positive correlation between the cooperative elongation of the mesocotyl and coleoptile and the seedling emergence rate in maize under deep-seeding environments, and its mesocotyl contributed more [2,49,50], supporting our findings in this study. We found an increase in seeding depth from 3 cm (CK(+)) to 20 cm (CK(-)), whereas the seedling emergence rate of both inbred lines (ly119-2 and ZRX87-1) decreased, with their mesocotyls and coleoptiles significantly elongated and slender and weaker seedlings (Figures 1 and 2).…”

Genome-Wide Association Study Identifies Quantitative Trait Loci and Candidate Genes Involved in Deep-Sowing Tolerance in Maize (Zea mays L.)

“…Under deep-sowing conditions, seeds can maintain a high germination rate, and strong seedling vigor is an important manifestation of their tolerance to deep sowing. The emergence rate of maize under deep-sowing conditions is significantly correlated with ML [ 13 , 14 , 15 , 16 ], followed by PL and SL [ 17 ]. In fact, longer plumules and shoots also indicate greater vitality of seeds and seedlings [ 18 ].…”

“…Therefore, to improve maize emergence and yield through deep sowing, maize seeds should have an elevated level of deep-sowing tolerance, which entails maintaining a high germination rate and good seedling vigor under deep-sowing conditions. Many studies have evaluated the deep-sowing tolerance of maize by measuring traits such as germination rate, mesocotyl length (ML), coleoptile length (CL), plumule length (PL), shoot length (SL), and primary root length (PRL) [ 13 , 14 , 15 , 16 ]. Among these traits, the emergence rate is the most straightforward metric for assessing the deep-sowing tolerance of maize, with higher rates corresponding to increased tolerance.…”

“…Consequently, some studies have combined RNA sequencing and meta-analysis to better dissect the genetics of deep-sowing tolerance in maize. Zhao et al [ 16 ] identified 13 major QTLs and 17 meta-QTLs associated with deep-sowing tolerance, along with 50 differentially expressed candidate genes within these QTLs. Wang et al [ 27 ] used transcriptome analysis to elucidate the molecular mechanisms of maize seed germination under deep-sowing conditions, identifying six candidate genes.…”

The Mechanism of Exogenous Salicylic Acid and 6-Benzylaminopurine Regulating the Elongation of Maize Mesocotyl

“…Lignin is the main component of the secondary cell wall. The change in lignin content and composition structure is directly related to the elasticity of the cell wall [ 26 ], and the increase in lignin content will have a negative impact on cell wall relaxation and cell elongation [ 57 ]. Therefore, the biosynthesis and metabolism of lignin play an important role in regulating the extension of maize mesocotyl cells.…”