Scientia Agricultura Sinica ›› 2022, Vol. 55 ›› Issue (16): 3071-3081.doi: 10.3864/j.issn.0578-1752.2022.16.001

• CROP GENETICS & BREEDING·GERMPLASM RESOURCES·MOLECULAR GENETICS • Previous Articles     Next Articles

Mining of Genetic Locus of Maize Stay-Green Related Traits Under Multi-Environments

CHANG LiGuo(),HE KunHui,LIU JianChao()   

  1. College of Agronomy, Northwest A&F University/Key Laboratory of Biology and Genetic Improvement of Maize in Arid Area of Northwest Region, Ministry of Agriculture and Rural Affairs/Maize Engineering Technology Research Centre of Shaanxi Province, Yangling 712100, Shaanxi
  • Received:2022-03-26 Accepted:2022-05-09 Online:2022-08-16 Published:2022-08-11
  • Contact: JianChao LIU E-mail:clg0601@163.com;ljcnwsuaf@nwsuaf.edu.cn

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Abstract:

【Objective】 Functional stay-green is generally considered a desirable trait in major crop varieties including maize. Finding new loci and candidate genes related to stay-green, and providing new theoretical basis for the genetic research on stay-green. 【Method】Using 150 recombinant inbred lines (RIL) populations derived from the cross between Xu 178 and K12, QTL mapping of three stay-green related traits (visual stay green (VSG), green leaf number at silking stage (GLNS) and green leaf number at mature stage (GLNM) were performed by the composite interval mapping（CIM）method of Windows QTL Cartographer V2.5. Besides, an association population, which composed of 139 natural materials genotyped with 50790 high-quality SNP markers, was used to dissect genetic locus of three traits by genome-wide association study (GWAS) based on the mixed linear model MLM). 【Result】Based on CIM, three traits (GLNM, GLNS and VSG)were mapped using phenotypic values in a single environment and best linear unbiased prediction (BLUP) value. A total of 37 QTLs were detected on all chromosomes except Chromosome 10, and the LOD score ranged from 2.58-11.36, with a phenotypic variation contribution rate of 4.34%-22.40%. Among them, 14, 12 and 11 loci were detected for GLNM, GLNS and VSG traits, respectively. Four of the QTLs, qGLNS2-1, qVSG1-1, qVSG1-2 and qVSG7-1, were genetically stable and were detected simultaneously in three or more different single environments. GWAS was performed on three stay-green related traits using MLM, and a total of 44 significant SNPs above the threshold line were detected. According to the physical position of SNP markers in the B73 reference genome, a total of 15 SNP were found to fall into the QTL interval mapped by linkage analysis. 【Conclusion】Combined with the results of QTL mapping and genome-wide association study, a total of 4 genetically stable colocalization genetic regions were detected (the corresponding physical position intervals on the B73 reference genome version 4 are 6.2-8.2 Mb on chromosome 1, 209.1-221.4 Mb on chromosome 2, 96.8-102.1 Mb on chromosome 6, and 4.9-11.4 Mb on chromosome 7), and four important candidate genes (Zm00001d006119, Zm00001d018975, Zm00001d006535 and Zm00001d036763) related to photosynthesis and stress response were mined.

Key words: maize (Zea mays L.), stay-green, genome-wide association study, QTL mapping

Table 1

Descriptive statistical analysis of phenotypic value among the RIL population"

性状
Traits		 环境
Env.		 亲本Parents 重组自交系RIL populations
许178
Xu 178		 K12 变异范围
Range		 均值±标准差
Mean±SD		 变异系数
CV (%)		 偏度
Skewness		 峰度
Kurtosis		 遗传力
H2 (%)
保绿度
VSG		 E1 4.70 1.70 1.00—5.00 3.10±0.20 36.81 0.12 -0.22 76.70
E2 4.31 1.32 1.00—5.00 2.71±0.21 42.40 0.37 -0.66
E3 5.00 2.04 1.00—5.00 2.92±0.33 43.42 0.26 0.10
E4 4.71 2.03 1.00—5.00 3.00±0.21 36.80 0.23 0.61
E5 5.00 2.30 1.00—5.00 2.80±0.20 40.31 0.31 0.64
E6 4.73 2.01 1.00—5.00 3.12±0.22 30.00 -0.29 -0.24
吐丝期绿叶数
GLNS		 E1 14.51 12.30 9.30—15.31 12.63±0.12 8.80 -0.33 0.69 75.60
E2 13.30 10.53 11.51—16.50 14.00±0.12 8.73 0.07 -0.65
E3 13.36 10.83 10.34—14.52 12.41±0.11 6.04 0.09 0.67
E4 13.00 12.08 7.81—14.00 11.00±0.13 9.52 -0.09 0.86
E5 15.32 12.50 11.00—15.83 13.41±0.14 7.81 -0.06 -0.22
E6 15.04 13.36 11.00—16.30 13.71±0.11 7.93 0.10 -0.41
成熟期绿叶数
GLNM		 E1 7.51 3.57 0.00—10.51 5.01±0.20 45.60 -0.39 -0.35 78.40
E2 10.00 3.86 0.00—9.00 3.22±0.21 71.54 0.48 -0.54
E3 10.31 4.53 0.00—11.81 4.40±0.30 76.52 0.22 -1.18
E4 10.22 4.32 0.00—9.80 5.83±0.22 39.63 -0.78 0.29
E5 11.83 3.50 0.00—9.52 3.25±0.21 79.20 0.55 -0.64
E6 4.01 2.50 2.02—13.31 9.23±0.22 20.34 -1.18 2.94

Fig. 1

Boxplots of phenotypic values of linkage populations(A-C) and association populations(D-F) under different environments E1: Yulin in 2014; E2: Yulin in 2015; E3: Yangling in 2014; E4: Yangling in 2015; E5: Huludao in 2014; E6: Huludao in 2015. e1: Yangling in 2016, e2: Yulin in 2016. VSG: Visual stay green; GLNS: Green leaf number at silking stage; GLNM: Green leaf number at mature stage. The same as below"

Fig. 2

Schematic diagram of QTL mapping for stay-green related traits A: Schematic diagram of the QTL distribution mapped in this study (orange, green, and purple represent visual stay green, green leaf number at mature stage and green leaf number at silking stage, respectively); B: The distribution of stay-green related QTL mapped by previous researchers"

Fig. 3

Manhattan plot and QQ plot of VSG (A), GLNS (B), GLNM (C) traits in e1 and e2 environments"

Table 2

Descriptive statistical analysis of phenotypic value among the association population"

性状 Traits 环境 Environments 范围 Range 均值±标准差 Mean±SD 偏度 Skewness 峰度 Kurtosis
保绿度
VSG		 e1 1.00—5.00 2.00±0.07 0.46 1.01
e2 1.00—5.00 3.66±0.09 -0.74 -0.38
吐丝期绿叶数
GLNS		 e1 8.50—15.60 11.93±0.11 0.25 0.11
e2 10.75—18.20 13.78±0.11 0.24 0.17
成熟期绿叶数
GLNM		 e1 0.00—11.90 2.59±0.17 1.21 1.47
e2 0.00—13.60 5.94±0.25 -0.15 -0.52
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