普通菜豆根系相关性状的关联分析
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摘要
幼苗期根系发育对作物的生长发育具有重要作用。利用生长袋纸培系统对324份普通菜豆种质的主根长、根干重、根体积、根表面积等9个根系相关性状进行表型鉴定,并结合覆盖全基因组、有多态性的116对SSR标记,利用MLM(Q+K)模型进行表型和标记的关联分析。表型分析表明,324份材料的9个根系相关性状表型变异丰富,平均变异系数的变动范围是10.09%～37.03%;基因型分析表明,116个多态性SSR标记共检测到919个等位变异位点,每个标记的平均基因多样性指数为0.59,多态性信息含量(PIC)平均值为0.54,显示这些标记具有较高的基因多样性;群体结构分析表明,供试材料分为两个亚群,与普通菜豆起源于两个基因库对应;关联分析结果显示,以P<0.01作为显著条件,共检测到48个显著标记位点,其中有10个位点同时与2个以上性状相关联,有5个位点与前人研究结果一致。研究结果为进一步理解普通菜豆根系的遗传机理提供了理论参考,也为分子标记辅助选择改良普通菜豆根系奠定了基础。
The root development at seeding stage plays an important role in crop growth and development. In this study, nine root-related traits such as taproot length, root dry weight, root volume and root surface area of 324 common bean accessions were examined by phenotyping using the growth bag paper culture system, and 116 polymorphic SSR(simple sequence repeats) markers covering the whole genome were performed by association analysis. Molecular markers and 9 root traits were analyzed by the program of MLM(mixed linear model) in Tassel 2.1 based on population structure and kinship. The results showed that the 324 common bean accessions were rich in phenotypic variation, and the average coefficient of variation(CV) ranged from 10.09% to 37.03%. Genotype analysis showed that 116 polymorphic SSR markers generated 919 allele loci. The range of genetic diversity index was from 0.0051 to 0.9098 with an average of 0.59. The average PIC(polymorphism information content) was 0.54 with range from0.0051 to 0.9033. The results indicated that these markers had larger genetic diversity among the alleles in common bean accessions. The population structure analysis indicated that 324 common bean varieties were divided into two subgroups, which were consistent with the theory of common beans originated from two gene banks. Association analysis showed that 48 significant marker loci were detected with P<0.01 as a significant condition. Among these loci, ten marker loci were associated with more than two root traits simultaneously, five marker loci were coincident with previous studies, 43 marker loci were verified as new associated loci. The results provide a theoretical basis for further understandings of the genetic mechanism of roots and provide a basis for improvement of root system by molecular-assisted breeding selection in common bean.
The root development at seeding stage plays an important role in crop growth and development. In this study, nine root-related traits such as taproot length, root dry weight, root volume and root surface area of 324 common bean accessions were examined by phenotyping using the growth bag paper culture system, and 116 polymorphic SSR(simple sequence repeats) markers covering the whole genome were performed by association analysis. Molecular markers and 9 root traits were analyzed by the program of MLM(mixed linear model) in Tassel 2.1 based on population structure and kinship. The results showed that the 324 common bean accessions were rich in phenotypic variation, and the average coefficient of variation(CV) ranged from 10.09% to 37.03%. Genotype analysis showed that 116 polymorphic SSR markers generated 919 allele loci. The range of genetic diversity index was from 0.0051 to 0.9098 with an average of 0.59. The average PIC(polymorphism information content) was 0.54 with range from0.0051 to 0.9033. The results indicated that these markers had larger genetic diversity among the alleles in common bean accessions. The population structure analysis indicated that 324 common bean varieties were divided into two subgroups, which were consistent with the theory of common beans originated from two gene banks. Association analysis showed that 48 significant marker loci were detected with P<0.01 as a significant condition. Among these loci, ten marker loci were associated with more than two root traits simultaneously, five marker loci were coincident with previous studies, 43 marker loci were verified as new associated loci. The results provide a theoretical basis for further understandings of the genetic mechanism of roots and provide a basis for improvement of root system by molecular-assisted breeding selection in common bean.
引文
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[27]Ochoa I E,Blair M W,Lynch J P. QTL Analysis of adventitious root formation in common bean under contrasting phosphorus availability.Crop Science,2006,46(4):1609-1621.
[28]周蓉,陈海峰,王贤智,等.大豆幼苗根系性状的QTL分析.作物学报,2011,37(7):1151-1158.
[29]Fang S Q,Yan X L,Liao H. 3D reconstruction and dynamic modeling of root architecture in situ and its application to crop phosphorus research. Plant Journal,2009,60(6):1096-1108.
[30]Hund A,Trachsel S,Stamp P. Growth of axile and lateral roots of maize:I development of a phenotying platform. Plant Soil,2009,325(1/2):335-349.
[31]Iyer-Pascuzzi A S,Symonova O,Mileyko Y,et al. Imaging and analysis platform for automatic phenotyping and trait ranking of plant root systems. Plant Physiology,2010,152(3):1148-1157.
[32]廖红,严小龙.菜豆根构型对低磷胁迫的适应性变化及基因型差异.植物学报,2000,42(2):158-163.
[33]Pritchard J K,Stephens M,Rosenberg N A,et al. Association mapping in structured populations. American Journal Human Genetics,2000,67(1):170-181.
[34]Zhao K Y,Aranzana M J,Kim S,et al. An Arabidopsis example of association mapping in structured samples. PLoS Genetics,2007,3(1):e4.
[35]Gepts P. Biochemical evidence bearing on the domestication of Phaseolus(Fabaceae)beans. Economic Botany,1990,44(S3):28-38.
[36]Zamani Z,Bahar M,Jacques M A,et al. Genetic diversity of the common bacterial blight pathogen of bean,Xanthomonas axonopodis pv. phaseoli,in Iran revealed by rep-PCR and PCR-RFLP analyses.World Journal Microbiology Biotechnology,2011,27(10):2371-2378.
[37]Yan X L,Liao H,Beebe S E,et al. QTL mapping of root hair and acid exudation traits and their relationship to phosphorus uptake in common bean. Plant Soil,2004,265(1/2):17-29.
[2]Rogers E D,Benfey P N. Regulation of plant root system architecture:implications for crop advancement. Current Opinion in Biotechnology,2015,32:93-98.
[3]Christopher J,Christopher M,Jennings R,et al. QTL for root angle and number in a population developed from bread wheats(Triticum aestivum)with contrasting adaptation to water-limited environments.Theoretical and Applied Genetics,2013,126(6):1563-1574.
[4]Hu B,Zhu C,Li F,et al. LEAF TIP NECROSIS1 plays a pivotal role in the regulation of multiple phosphate starvation responses in rice.Plant Physiology,2011,156(3):1101-1115.
[5]Ku L X,Sun Z H,Wang C L,et al. QTL mapping and epistasis analysis of brace root traits in maize. Molecular Breeding,2011,30(2):697-708.
[6]Li R,Han Y,Lv P,et al. Molecular mapping of the brace root traits in sorghum(Sorghum bicolor L. Moench). Breeding Science,2014,64(2):193-198.
[7]Mace E S,Singh V,Van Oosterom E J,et al. QTL for nodal root angle in sorghum(Sorghum bicolor L. Moench)co-locate with QTL for traits associated with drought adaptation. Theoretical and Applied Genetics,2012,124(1):97-109.
[8]Zheng X,Chen B,Lu G,et al. Overexpression of a NAC transcription factor enhances rice drought and salt tolerance. Biochemical and Biophysical Research Communications,2009,379(4):985-989.
[9]Asfaw A,Blair M W. Quantitative trait loci for rooting pattern traits of common beans grown under drought stress versus non-stress conditions. Molecular Breeding,2011,30(2):681-695.
[10]Beebe S E,Rojas-Pierce M,Yan X,et al. Quantitative trait loci for root architecture traits correlated with phosphorus acquisition in common bean. Crop Science,2006,46(1):413-423.
[11]Lopez-Marin H D,Rao I M,Blair M W. Quantitative trait loci for root morphology traits under aluminum stress in common bean(Phaseolus vulgaris L.). Theoretical and Applied Genetics,2009,119(3):449-458.
[12]Abenavoli M R,Leone M,Sunseri F,et al. Root phenotyping for drought tolerance in bean landraces from Calabria(Italy). Journal of Agronomy and Crop Science,2016,202(1):1-12.
[13]Polania J,Poschenrieder C,Rao I,et al. Root traits and their potential links to plant ideotypes to improve drought resistance in common bean. Theoretical and Experimental Plant Physiology,2017,29(3):143-154.
[14]Roman-Aviles B,Snapp S S,Kelly J D. Assessing root traits associated with root rot resistance in common bean. Field Crop Research,2004,86(2/3):147-156.
[15]Sofi P A,Saba I. Natural variation in common bean(Phaseolus vulgaris L.)for root traitsand biomass partitioning under drought.Indian Journal of Agricultural Research,2016,50(6):604-608.
[16]Tsuji W,Inanaga S,Araki H,et al. Development and distribution of root system in two grain sorghum cultivars originated from Sudan under drought stress. Plant Production Science,2005,8(5):553-562.
[17]孙广玉,何庸,张荣华.大豆根系生长和活性特点的研究.大豆科学,1996,15(4):317-321.
[18]Liao H,Rubio G,Yan X L,et al. Effect of phosphorus availability on basal root shallowness in common bean. Plant Soil,2001,232(1/2):69-79.
[19]Armengaud P,Zambaux K,Hills A,et al. EZ-Rhizo:integrated software for the fast and accurate measurement of root system architecture. Plant Journal,2009,57(5):945-956.
[20]Li X M,Yuan D J,Wang H T,et al. Increasing cotton genome coverage with polymorphic SSRs as revealed by SSCP. Genome,2012,55(6):459-470.
[21]Chen M L,Wu J,Wang L F,et al. Development of mapped simple sequence repeat markers from common bean(Phaseolus vulgaris L.)based on genome sequences of a Chinese landrace and diversity evaluation. Molecular Breeding,2014,33(2):489-496.
[22]Kami J,Velásquez V B,Debouck D G,et al. Identification of presumed ancestral dna sequences of phaseolin in phaseolus vulgaris. Proceedings of the National Academy of Sciences of the United States of America,1995,92(4):1101-1104.
[23]Liu K J,Muse S V. PowerMarker:an integrated analysis environment for genetic marker analysis. Bioinformatics,2005,21(9):2128-2129.
[24]Evanno G,Regnaut S,Goudet J. Detecting the number of clusters of individuals using the software STRUCTURE:a simulation study.Molecular Ecology,2005,14(8):2611-2620.
[25]Hardy O J,Vekemans X. SPAGEDi:a versatile computer program to analyse spatial genetic structure at the individual or population levels. Molecular Ecology Notes,2002,2(4):618-620.
[26]Bradbury P J,Zhang Z,Kroon D E,et al. TASSEL:software for association mapping of complex traits in diverse samples.Bioinformatics,2007,23(19):2633-2635.
[27]Ochoa I E,Blair M W,Lynch J P. QTL Analysis of adventitious root formation in common bean under contrasting phosphorus availability.Crop Science,2006,46(4):1609-1621.
[28]周蓉,陈海峰,王贤智,等.大豆幼苗根系性状的QTL分析.作物学报,2011,37(7):1151-1158.
[29]Fang S Q,Yan X L,Liao H. 3D reconstruction and dynamic modeling of root architecture in situ and its application to crop phosphorus research. Plant Journal,2009,60(6):1096-1108.
[30]Hund A,Trachsel S,Stamp P. Growth of axile and lateral roots of maize:I development of a phenotying platform. Plant Soil,2009,325(1/2):335-349.
[31]Iyer-Pascuzzi A S,Symonova O,Mileyko Y,et al. Imaging and analysis platform for automatic phenotyping and trait ranking of plant root systems. Plant Physiology,2010,152(3):1148-1157.
[32]廖红,严小龙.菜豆根构型对低磷胁迫的适应性变化及基因型差异.植物学报,2000,42(2):158-163.
[33]Pritchard J K,Stephens M,Rosenberg N A,et al. Association mapping in structured populations. American Journal Human Genetics,2000,67(1):170-181.
[34]Zhao K Y,Aranzana M J,Kim S,et al. An Arabidopsis example of association mapping in structured samples. PLoS Genetics,2007,3(1):e4.
[35]Gepts P. Biochemical evidence bearing on the domestication of Phaseolus(Fabaceae)beans. Economic Botany,1990,44(S3):28-38.
[36]Zamani Z,Bahar M,Jacques M A,et al. Genetic diversity of the common bacterial blight pathogen of bean,Xanthomonas axonopodis pv. phaseoli,in Iran revealed by rep-PCR and PCR-RFLP analyses.World Journal Microbiology Biotechnology,2011,27(10):2371-2378.
[37]Yan X L,Liao H,Beebe S E,et al. QTL mapping of root hair and acid exudation traits and their relationship to phosphorus uptake in common bean. Plant Soil,2004,265(1/2):17-29.