Genome-wide Association Study of Chlorophyll Content in Maize Leaves

doi:10.13560/j.cnki.biotech.bull.1985.2017.04.013

Abstract

Abstract: The chlorophyll content of plant leaves is closely related to photosynthetic efficiency and yield potential,thus it is an important physiological indicator of all crop species. However,currently most cloned genes controlling chlorophyll content are from Arabidopsis and rice,and the genetic basis of natural variation in chlorophyll content in maize is still unclear. In this research it was discovered that the chlorophyll content of the first leaves at the seedling stage was highly correlated with that of ear leaves at silking stage,and the former had a higher heritability than the latter. This study further analyzed the chlorophyll contents of first leaves from 287 maize inbred lines. Genome-wide association study using 558 269 SNP markers revealed 9 SNPs significantly associated with the measured trait,leading to the discovery of 16 candidate genes. Two genes potentially controlling chlorophyll content in maize were identified by sequence analysis and functional annotation of these candidate genes：a homolog of the Arabidopsis Tic22 and a homolog of rice SAG12 relating to aging.

Key words: maize, chlorophyll content, GWAS

TENG Shou-zhen, WANG Hai, LIANG Hai-sheng, XIN Hong-jia, LI Sheng-yan, LANG Zhi-hong. Genome-wide Association Study of Chlorophyll Content in Maize Leaves[J]. Biotechnology Bulletin, 2017, 33(4): 98-107.

References

[1] Yan JB, Warburton M, Crouch J. Association mapping for enhancing maize（Zea mays L. ）genetic improvement[J]. Crop Science, 2011, 51（2）：433-449.
[2] Zhang X, Zhang H, Li LJ, et al. Characterizing the population structure and genetic diversity of maize breeding germplasm in Southwest China using genome-wide SNP markers[J]. BMC Genomics, 2016, 17（1）：697.
[3] Jannink J, Bink MC, Jansen RC. Using complex plant pedigrees to map valuable genes[J]. Trends in Plant Science, 2001, 6（8）：337-342.
[4] Zondervan KT, Cardon LR. The complex interplay among factors that influence allelic association[J]. Nature Reviews Genetics, 2004, 5（2）：89-100.
[5] 李玮瑜, 张斌, 张嘉楠, 等 . 利用关联分析发掘小麦自然群体旗叶叶绿素含量的优异等位变异[J]. 作物学报, 2012, 38（6）：962-970.
[6] 刘贞琦, 刘振业, 马达鹏, 等 . 水稻叶绿素含量及其与光合速率关系的研究[J]. 作物学报, 1984, 10（1）：57-62.
[7] 左宝玉, 李世仪, 匡廷云, 等 . 玉米不同层次叶片叶绿体的超微结构和叶绿素含量变化[J]. 作物学报, 1987, 13（3）：213-218.
[8] Masuda T, Fujita YC. Regulation and evolution of chlorophyll metabolism[J]. Photochemical & Photobiological Sciences, 2008, 7（7）：1131-1149.
[9] Peng SB, Gurdevs K, Parminder V, et al. Progress in ideotype breeding to increase rice yield potential[J]. Field Crops Research, 2008, 108（1）：32-38.
[10] Wang F, Wang G, Li X, et al. Heredity, physiology and mapping of a chlorophyll content gene of rice（Oryza sativa L. ）[J]. Journal of Plant Physiology, 2008, 165（3）：324-330.
[11] Huang JL, Qin F, Zang GC, et al. Mutation of OsDET1 increases chlorophyll content in rice[J]. Plant Science, 2013, 210：241-249.
[12] Huang JY, Wang YF, Yang JS. Over-expression of OsPSK3 increases chlorophyll content of leaves in rice[J]. Hereditas, 2010, 32（12）：1281-1289.
[13] Wang QX, Xie WB, Xing HK, et al. Genetic architecture of natural variation in rice chlorophyll content revealed by a genome-wide association study[J]. Molecular Plant, 2015, 8（6）：946-957.
[14] Zhu X, Chen J, Xie Z, et al. Jasmonic acid promotes degreening via MYC2/3/4- and ANAC019/055/072-mediated regulation of major chlorophyll catabolic genes[J]. Plant Journal, 2015, 84（3）：597-610.
[15] Yang JD, Worley E, Udvardi M. A NAP-AAO3 regulatory module promotes chlorophyll degradation via ABA biosynthesis in Arabidopsis leaves[J]. Plant Cell, 2014, 26（12）：4862-4874.
[16] Gao S, Gao J, Zhu X, et al. ABF2, ABF3 and ABF4 promote ABA-mediated chlorophyll degradation and leaf senescence by transcriptional activation of chlorophyll catabolic genes and senescence-associated genes in Arabidopsis[J]. Molecular Plant, 2016, 9（9）：1272-1285.
[17] Sakuraba Y, Park SY, Kim YS, et al. Arabidopsis STAY-GREEN2 is a negative regulator of chlorophyll degradation during leaf senescence[J]. Molecular Plant, 2014, 7（8）：1288-1302.
[18] Zhang LG, Kusaba M, Tanaka A, et al. Protection of chloroplast membranes by VIPP1 rescues aberrant seedling development in Arabidopsis nyc1 mutant[J]. Frontiers in Plant Science, 2016, 7（73）：533.
[19] Ma QH, Liu YC. Expression of isopentenyl transferase gene（ipt）in leaf and stem delayed leaf senescence without affecting root growth[J]. Plant Cell Reports, 2009, 28（11）：1759-1765.
[20] Chang C, Lu J, Zhang HP, et al. Copy number variation of cytokinin oxidase gene Tackx4 associated with grain weight and chlorophyll content of flag leaf in common wheat[J]. PLoS One, 2015, 10 （12）：e0145790.
[21] Gitelson AA, Peng Y. Efficiency of chlorophyll in gross primary productivity：A proof of concept and application in crops[J]. Journal of Plant Physiology, 2016, 201：101-110.
[22] Wagle P, Zhang Y, Jin C, et al. Comparison of solar-induced chlorophyll fluorescence, light-use efficiency, and process-based GPP models in maize[J]. Ecological Applications, 2016, 26（4）：1211-1222.
[23] Bradbury PJ, Zhang Z, Kroon DE, et al. TASSEL：Software for association mapping of complex traits in diverse samples[J]. Bioinformatics, 2007, 23：2633-2635.
[24] Kasmati AR, Töpel M, Khan NZ, et al. Evolutionary, molecular and genetic analyses of Tic22 homologues in Arabidopsis thaliana chloroplasts[J]. PLoS One, 2013, 8（5）：e63863.
[25] Rudolf M, Machettira AB, Groβ LE, et al. In vivo function of Tic22, a protein import component of the intermembrane space of chloroplasts[J]. Molecular Plant, 2013, 6（3）：817-829.
[26] Singh S, Singh A, Nandi AK. The rice OsSAG12-2 gene codes for a functional protease that negatively regulates stress-induced cell death[J]. Journal of Biosciences, 2016, 41（3）：1-9.
[27] Otegui MS, Yoo-Sun N, Martínez DE, et al. Senescence-associated vacuoles with intense proteolytic activity develop in leaves of Arabidopsis and soybean[J]. Plant Journal, 2005, 41（6）：831-844.