Welcome to Acta Agronomica Sinica，

Acta Agron Sin ›› 2012, Vol. 38 ›› Issue (06): 962-970.doi: 10.3724/SP.J.1006.2012.00962

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

Exploring Elite Alleles for Chlorophyll Content of Flag Leaf in Natural Population of Wheat by Association Analysis

LI Wei-Yu1,2,ZHANG Bin2,ZHANG Jia-Nan2,3,CHANG Xiao-Ping2, LI Run-Zhi1,*,JING Rui-Lian2,*   

  1. 1 Agronomy College, Shanxi Agricultural University, Taigu 030801, China; 2 National Key Facility for Crop Gene Resources and Genetic Improvement / Key Laboratory of Crop Germplasm Utilization, Ministry of Agriculture / Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China; 3 National Millet Improvement Center of China, Institute of Millet Crops / Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang 050031, China
  • Received:2012-01-19 Revised:2012-04-18 Online:2012-06-12 Published:2012-04-23
  • Contact: 景蕊莲, E-mail: jingrl@caas.net.cn, Tel: 010-82105829; 李润植, E-mail: rli2001@hotmail.com

PDF

2282

Cited

12

Abstract: Elite alleles associated with chlorophyll content of flag leaf in a natural population of winter wheat (Triticum aestivum L.) consisting of 262 accessions were measured at flowering and grain-filling stages under both rainfed and well-watered conditions in two experimental locations in Beijing, China. A total of 169 SSR markers distributed on the 21 chromosomes of wheat were employed to detect the genetic diversity and genetic structure of the population. Association analysis between SSR loci and chlorophyll content trait was performed using TASSEL MLM (mixed linear model) program. The phenotypic allele effect was estimated through comparing the average phenotypic value over accessions with that of “null allele”. A total of 2048 alleles were identified on the 169 SSR loci, and each locus had 2–37 alleles with an average of 12. The polymorphism information contents (PICs) of the SSR loci ranged from 0.008 to 0.936 with an average of 0.628. Forty markers were found to be significantly associated with chlorophyll content (P<0.001) on 22 loci, of which 11 markers showed repeated associations, particularly, loci Xwmc419-1B and Xgwm501-2B had associations for three times. The alleles on loci Xcfa2123-7A, Xgwm232-1D, and Xgwm429-2B exhibited more than 4.0 of phenotypic effect value.

Key words: Wheat (Triticum aestivum L.), Chlorophyll content, SSR, Association analysis, Allelic variation

[1]Reynolds M, Foulkes M J, Slafer G A, Berry P, Parry M A J, Snape J W, Angus W J. Raising yield potential in wheat. J Exp Bot, 2009, 60: 1899?1918

[2]Borrell A K, Tao Y, Mcintyre C L. Physiological basis, QTL and MAS of the stay-green drought resistance trait in grain sorghum. CIMMYT, Mexico, DF (Mexico), 2000. pp 142?146

[3]Yang D L, Jing R L, Chang X P, Li W. Quantitative trait loci mapping for chlorophyll fluorescence and associated traits in wheat (Triticum aestivum L.). J Integr Plant Biol, 2007, 49: 646?654

[4]Bijanzadeh E, Emam Y. Effect of defoliation and drought stress on yield components and chlorophyll content of wheat. Pak J Biol Sci, 2010, 13: 699?705

[5]Khamssi N N, Najaphy A. Comparison of photosynthetic components of wheat genotypes under rain-fed and irrigate conditions. Photochem Photobiol, 2012, 88: 76?80

[6]Jiang G H, He Y Q, Xu C G, Li X H, Zhang Q. The genetic basis of stay-green in rice analyzed in a population of doubled haploid lines derived from an indica by japonica cross. Theor Appl Genet, 2004, 108: 688?698

[7]Jannink J L, Bink M C A M, Jansen R C. Using complex plant pedigrees to map valuable genes. Trends Plant Sci, 2001, 6: 337?342

[8]Risch N J. Searching for genetic determinants in the new millennium. Nature, 2000, 405: 847?856

[9]Zondervan K T, Cardon L R. The complex interplay among factors that influence allelic association. Nat Rev Genet, 2004, 5: 89?100

[10]de Oliveira Borba T C, Brondani R P V, Breseghello F, Coelho A S G, Mendonca J A, Rangel P H N, Brondani C. Association mapping for yield and grain quality traits in rice (Oryza sativa L). Genet Mol Biol, 2010, 33: 515?524

[11]Huang X H, Zhao Y, Wei X H, Li C, Wang A, Zhao Q, Li W J, Guo Y L, Deng L W, Zhu C R, Fan D L, Lu Y Q, Weng Q J, Liu K Y, Zhou T Y, Jing Y F, Si L Z, Dong G J, Huang T, Lu T T, Feng Q, Qian Q, Li J Y, Han B. Genome-wide association study of flowering time and grain yield traits in a worldwide collection of rice germplasm. Nat Genet, 2011, 44: 32?39

[12]Kump K L, Bradury P J, Wisser R J, Buckler E S, Bclcher A R, Oropeza-Rosas M A, Zwonitzer J C, Kresovich S, McMullen M D, Ware D, Balint-Kurti P J, Holland J. Genome-wide association study of quantitative resistance to southern leaf blight in the maize nested association mapping population. Nat Genet, 2011, 43: 163?168

[13]Yan J B, Shah T, Warburton M L, Buckler E S, McMullen M D, Crouch J. Genetic characterization and linkage disequilibrium estimation of a global maize collection using SNP markers. PLoS One, 2009, 4: e8451

[14]Breseghello F, Sorrells M E. Association mapping of kernel size and milling quality in wheat (Triticum aestivum L.) cultivars. Genetics, 2006, 172: 1165?1177

[15]Wang L F, Ge H M, Hao C Y, Dong Y S, Zhang X Y. Identifying loci influencing 1 000-kernel weight in wheat by microsatellite screening for evidence of selection during breeding. PLoS One, 2012, 7: e29432

[16]Wei T-M(魏添梅), Chang X-P(昌小平), Min D-H(闵东红), Jing R-L(景蕊莲). Analysis of genetic diversity and tapping elite alleles for plant height in drought-tolerant wheat varieties. Acta Agron Sin (作物学报), 2010, 36(6): 895?904 (in Chinese with English abstract)

[17]Zhang J N, Hao C Y, Ren Q, Chang X P, Liu G R, Jing R L. Association mapping of dynamic developmental plant height in common wheat. Planta, 2011, 235: 891?902

[18]Somers D J, Isaac P, Edwards K. A high-density microsatellite consensus map for bread wheat (Triticum aestivum L.). Theor Appl Genet, 2004, 109: 1105?1114

[19]Holland J B, Nyquist W E, Cervantes-Martínez C T. Estimating and interpreting heritability for plant breeding: an update. Plant Breed Rev, 2003, 22: 9?112

[20]Liu K, Muse S V. PowerMarker: an integrated analysis environment for genetic marker analysis. Bioinformatics, 2005, 21: 2128?2129

[21]Evanno G, Regnaut S, Goudet J. Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Mol Ecol, 2005, 14: 2611?2620

[22]Bradbury P J, Zhang Z, Kroon D E, Casstevens T M, Ramdoss Y, Buckler E S. TASSEL: software for association mapping of complex traits in diverse samples. Bioinformatics, 2007, 23: 2633?2635

[23]Hardy O J, Vekemans X. SPAGeDi: a versatile computer program to analyse spatial genetic structure at the individual or population levels. Mol Ecol Notes, 2002, 2: 618?620

[24]Wen Z-X(文自翔), Zhao T-J(赵团结), Zheng Y-Z(郑永战), Liu S-H(刘顺湖), Wang C-E(王春娥), Wang F(王芳), Gai J-Y(盖钧镒). Association analysis of agronomic and quality traits with SSR markers in Glycine max and Glycine soja in China: I. Population structure and associated markers. Acta Agron Sin (作物学报), 2008, 34(7): 1169?1178 (in Chinese with English abstract)

[25]Wen Z-X(文自翔), Zhao T-J(赵团结), Zheng Y-Z(郑永战), Liu S-H(刘顺湖), Wang C-E(王春娥), Wang F(王芳), Gai J-Y(盖钧镒). Association analysis of agronomic and quality traits with SSR markers in Glycine max and Glycine soja in China: II. Exploration of elite alleles. Acta Agron Sin (作物学报), 2008, 34(8): 1339?1349 (in Chinese with English abstract)

[26]Zhang X-Y(张学勇), Tong Y-P(童依平), You G-X(游光霞), Hao C-Y(郝晨阳), Ge H-M(盖红梅), Wang L-F(王兰芬), Li B(李滨), Dong Y-C(董玉琛), Li Z-S(李振声). Hitchhiking effect mapping: A new approach for discovering agronomic important genes. Sci Agric Sin (中国农业科学), 2006, 39(8): 1526?1535 (in Chinese with English abstract)

[27]Doebley J F, Gaut B S, Smith B D. The molecular genetics of crop domestication. Cell, 2006, 127: 1309?1322

[28]Subudhi P K, Rosenow D T, Nguyen H T. Quantitative trait loci for the stay green trait in sorghum (Sorghum bicolor L.): consistency across genetic backgrounds and environments. Theor Appl Genet, 2000, 101: 733?741

[29]Van Oosteerom E J, Jayachandran R, Bidinger F R. Diallel analysis of the stay-green trait and its components in sorghum. Crop Sci, 1996, 36: 540?555

[30]Walulu R S, Rosenow D T, Wester D B, Nguyen H T. Inheritance of the stay-green trait in sorghum. Crop Sci, 1994, 34: 970?972

[31]Jiang G H, He Y Q, Xu C G, Li X H, Zhang Q. The genetic basis of stay-green in rice analyzed in a population of doubled haploid lines derived from an indica by japonica cross. Theor Appl Genet, 2004, 108: 688?698

[32]Hui Z(惠振). The Photosynthetic Characteristic of TaSG1 Wheat Mutant with Stay-Green Phenotype and the Physiological Mechanism Responsible for Stay-Green. MS Thesis of Shandong Agricultural University, 2009. p 59 (in Chinese with English abstract)

[33]Rafalski A. Applications of single nucleotide polymorphisms in crop genetics. Curr Opin Plant Biol, 2002, 5: 94?100

[34]Lou X Y, Casella G, Littell R C, Yang M C K, Johnson J A, Wu R L. A haplotype-based algorithm for multilocus linkage disequilibrium mapping of quantitative trait loci with epistasis. Genetics, 2003, 163: 1533?1548

[35]Yang D-L(杨德龙). Genetic Dissection of Quantitive Loci for Important Physiological and Agronomic Traits Associated with Drought Tolerance in Wheat (Triticum aestivum L.). PhD Dissertation of Gansu Agricultural University, 2007. pp 27?31 (in Chinese with English abstract)

[36]Jing R-L(景蕊莲), Chang X-P(昌小平), Jia J-Z(贾继增), Hu R-H(胡荣海). Establishing wheat doubled haploid population for genetic mapping by anther culture. Biotechnology (生物技术), 1999, 9(3): 4?8 (in Chinese)

[37]Zhang K, Zhang Y, Chen G, Tian J. Genetic analysis of grain yield and leaf chlorophyll content in common wheat. Cereal Res Commun, 2009, 37: 499?511

[38]Thornsberry J M, Goodman M M, Doebley J, Kresovich S, Nielsen D, Buckler IV E S. Dwarf8 polymorphisms associate with variation in flowering time. Nat Genet, 2001, 28: 286?289

[39]Yu J, Buckler E S. Genetic association mapping and genome organization of maize. Curr Opin Biotechnol, 2006, 17: 155?160

[40]Flint-Garcia S A, Thuillet A, Yu J, Pressoir G, Romero S M, Mitchell S E, Doebley J, Kresovich S, Goodman M. M, Buckler E S. Maize association population: a high-resolution platform for quantitative trait locus dissection. Plant J, 2005, 44: 1054?1064
[1] Yan An, Jiang Kun-Wei, Wang Rong-Yuan, Tian Lin, Zhang Lu, Wang Yun, Xu Jian-Long. Identification and cloning of SVN7 controlling small vascular bundle number in the rice flag leaf [J]. Acta Agronomica Sinica, 2026, 52(5): 1364-1372.
[2] Zhang Ying-Xing, Bheel Chander Kumar, Song Yu-Zhen, Wang Yue, Cao Yue, Khound Rituraj, Santra Dipak Kumar, Cao Xiao-Ning, Wang Rui-Yun. Screening and phenotypic characterization of EMS-induced mutants with elite agronomic traits in broomcorn millet [J]. Acta Agronomica Sinica, 2026, 52(5): 1388-1400.
[3] Tian Chun-Yan, Lu Xin, Wu Cai-Wen, Xu Chao-Hua, Liu Jia-Yong, Bian Xin, Tao Lian-An. Genetic diversity analysis and breeding potential evaluation of innovative sugarcane germplasm based on fluorescent SSR [J]. Acta Agronomica Sinica, 2026, 52(4): 1057-1072.
[4] Zhang Chao, Guo Huan, Li Zhong-Ling, Yue Shu-Ning, Zhao Na. Mapping genes associated with anthocyanin in maize kernels using BSA-seq technology [J]. Acta Agronomica Sinica, 2026, 52(3): 780-789.
[5] LI Lu-Qi, CHENG Yu-Kun, BAI Bin, LEI Bin, GENG Hong-Wei. Genome-wide association analysis of stomatal-related traits in wheat leaves [J]. Acta Agronomica Sinica, 2025, 51(9): 2266-2284.
[6] LI Yun-Xiang, GUO Qian-Qian, HOU Wan-Wei, ZHANG Xiao-Juan. Genome-wide association analysis of drought resistance traits in wheat seedlings introduced from ICARDA [J]. Acta Agronomica Sinica, 2025, 51(9): 2387-2398.
[7] CAI Jin-Shan, LI Chao-Nan, WANG Jing-Yi, LI Ning, LIU Yu-Ping, JING Rui-Lian, LI Long, SUN Dai-Zhen. Genome-wide association study of root traits in wheat seedlings and identification of a superior allele at TaSRL-3B [J]. Acta Agronomica Sinica, 2025, 51(8): 2020-2032.
[8] LI Wen-Jia, LIAO Yong-Jun, HUANG Lu, LU Qing, LI Shao-Xiong, CHEN Xiao-Ping, JIN Jing-Wei, WANG Run-Feng. Genome-wide associate analysis of flowering traits and identification of candidate genes in peanut [J]. Acta Agronomica Sinica, 2025, 51(5): 1400-1408.
[9] WANG Ya-Wen, QI Zheng-Yang, YOU Jia-Qi, NIE Xin-Hui, CAO Juan, YANG Xi-Yan, TU Li-Li, ZHANG Xian-Long, WANG Mao-Jun. Preparation of cotton 60K functional locus gene chip and its application to genetic research [J]. Acta Agronomica Sinica, 2025, 51(5): 1178-1188.
[10] XU Jian-Xia, DING Yan-Qing, CAO Ning, CHENG Bin, GAO Xu, LI Wen-Zhen, ZHANG Li-Yi. Genome-wide association analysis and prediction of candidate genes for plant height and internode number in Chinese sorghum [J]. Acta Agronomica Sinica, 2025, 51(3): 568-585.
[11] GUO Shu-Hui, PAN Zhuan-Xia, ZHAO Zhan-Sheng, YANG Liu-Liu, HUANG-FU Zhang-Long, GUO Bao-Sheng, HU Xiao-Li, LU Ya-Dan, DING Xiao, WU Cui-Cui, LAN Gang, LYU Bei-Bei, TAN Feng-Ping, LI Peng-Bo. Genetic analysis of a major fiber length locus on chromosome D11 of upland cotton [J]. Acta Agronomica Sinica, 2025, 51(2): 383-394.
[12] WANG Hao-Chen, WANG Ke-Jing, HAN Juan, LI Xiang-Hua. Spatial genetic structure characteristics of natural populations of Glycine tomentella in two representative habitats in the southeast coast, China: a study of intrapopulation sampling strategy [J]. Acta Agronomica Sinica, 2025, 51(11): 2875-2885.
[13] WANG Jian-Peng, JIAO Hui-Min, CHENG Yu-Kun, MA Meng-Yao, GENG Hong-Wei. Determination of SOD activity and allelic variation at the TaSOD-B2 locus in Xinjiang wheat [J]. Acta Agronomica Sinica, 2025, 51(10): 2705-2712.
[14] ZHENG Dong, ZHOU Xian-Li, TENG Chang-Cai, HOU Wan-Wei, ZHANG Hong-Yan, LIU Yu-Jiao. Genetic relationship analysis and fingerprints construction of faba bean varieties in Qinghai province based on SSR markers [J]. Acta Agronomica Sinica, 2025, 51(1): 79-90.
[15] KUANG Bo-Wen, WEI Ni, LIU Jin-Dian, CHEN Mei-Yan, MAO Xing-Jie, DUAN Wei-Xing, YANG Xi-Ping. Development of SSR markers and database based on genomes of sugarcane and its relatives [J]. Acta Agronomica Sinica, 2025, 51(1): 103-116.
Viewed
Full text


Abstract

Cited
  Shared   
  Discussed   
No Suggested Reading articles found!
Add: No. 80 Xueyuan South Rd, Beijing 100081, P. R. China E-mail: zwxb301@caas.cn
Supported by Beijing Magtech Co.Ltd