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Acta Prataculturae Sinica ›› 2021, Vol. 30 ›› Issue (5): 103-120.DOI: 10.11686/cyxb2020295

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QTL mapping and candidate gene analysis of leaf area in maize (Zea mays) under different watering environments

Xiao-qiang ZHAO1(), Yuan ZHONG1(), Wen-qi ZHOU2   

  1. 1.Gansu Provincial Key Laboratory of Aridland Crop Science,Gansu Agricultural University,Lanzhou 730070,China
    2.Crop Research Institute,Gansu Academy of Agricultural Sciences,Lanzhou 730070,China
  • Received:2020-06-29 Revised:2020-08-31 Online:2021-05-20 Published:2021-04-16
  • Contact: Yuan ZHONG

Abstract:

Leaf area (LA) and its distribution influences the efficiency of photosynthesis and transpiration rate, and is also closely related to drought tolerance, planting density, degree of lodging and grain yield in maize (Zea mays). In-depth analysis of the molecular mechanisms controlling LA under different moisture levels at different growth stages is of great significance for the breeding of drought tolerant and high-yielding new maize varieties. In this study, composite interval mapping (CIM) and mixed linear model mapping based on composite interval mapping (MCIM) was carried out across two F2∶3 populations under eight different ‘environments’. Specifically, experiments were set up in Gansu Province between 1508 and 1785 m altitude at Wuwei and Zhangye in 2014 and Gulang and Jingtai in 2015, and each of the four experiments had contrasting fully watered and moisture deficit treatments. Quantitative trait loci (QTLs) for LA (determined by measuring the 10th-12th leaves in late vegetative and three ear-leaves in early reproductive growth stages) were analyzed in single environments and across all environments. The candidate genes in the stable QTLs (sQTLs) were identified and the corresponding gene functions were determined using the reference genome B73 RefGen_v3. A total of seven QTLs were identified by CIM mapping cross vegetative and reproductive growth stages of the two F2∶3 populations in all eight environments, five of these in fully watered treatments, five in moisture deficit treatments and three shared by both fully watered and moisture deficit treatments. These QTLs exhibited dominance (81.0%), partial-dominance (14.3%), and over-dominance (4.7%) effects. Six joint QTLs for LA were found among all environments by joint analysis with MCIM, three from each of the two populations. One QTL was involved in a significant QTL by environment interaction (QTL×E; Bin 2.08-2.09), and one significant epistasis (Bin 1.08-1.10 and Bin 2.08-2.09) was mapped with an additive by additive (AA) effect. Combining CIM and MCIM methods for further analysis, six stable QTLs (sQTLs) were detected in Bin 1.08-1.10, Bin 2.08-2.09, Bin 4.08-4.09, Bin 6.05, Bin 8.03, and Bin 10.03, and 12 candidate genes that regulated leaf development in maize were located in these sQTL intervals. From bioinformatic data, 75 candidate genes related to leaf development were collected and their phylogenetic tree constructed. The phylogenetic tree of these 75 genes comprised three major evolutionary branches, and the 12 candidate genes identified above were distributed on the three branches. These results lay a foundation for systematic understanding of the molecular mechanisms governing LA in different environments at different plant growth stages. These detected sQTLs identify important genomic regions for LA improvement, and the detected candidate genes can provide reference sequences for further gene cloning, functional analysis, and other breeding applications.

Key words: Zea mays, leaf area, drought, QTL, candidate gene