陆地棉低世代群体纤维品质QTL定位及候选基因功能注释
|
摘要
【目的】通过对纤维品质数量性状位点(Quantitative trait loci,QTLs)定位及其基因功能注释,为分子标记辅助育种提供理论依据。【方法】以2个纤维品质有差异的陆地棉品种(系)中棉所49和396289为亲本构建F2群体,以高密度遗传图谱为基础,对3个环境的F2:3家系做包括细度和成熟度等在内的7个纤维品质性状QTLs定位,利用直系同源基因簇(Clusters of orthologous groups,COG)、基因本体(Gene ontology,GO)和京都基因与基因组百科全书(Kyoto encyclopedia of genes and genomes,KEGG)等数据库对QTLs做基因功能注释。【结果】获得157个与纤维品质有关的QTLs,分布于20条染色体上,A03、A04、D02、A11和D07等有较多性状的QTLs聚集,可能是控制纤维品质性状的关键染色体。共获得13个稳定QTLs,其中qFL-A03-1和qFin-A11-4在3个环境中重复出现,另有9个QTLs则在2个环境中重复出现。通过COG、GO和KEGG对QTLs进行基因功能注释,共获得4 763个候选基因,3个数据库分别注释到2 416、4 188和2 512个基因,在稳定QTLs中共注释到429个基因,其中一些基因可能与纤维品质关系密切。【结论】利用高通量测序获得的高密度遗传图谱有助于获得较多QTLs,有利于纤维品质相关候选基因的筛选及性状的改良,提高育种效率。
[Objective] This article aims to provide a theoretical basis for molecular marker-assisted breeding by quantitative trait loci(QTLs) mapping and gene function annotation of fiber quality. [Method] F2 populations were constructed using the two cotton cultivars(lines), CCRI 49 and 396289, as parents. Based on high-density genetic maps, the F2:3 families with three environments were included in the F2 population. The QTL mapping of seven fiber quality traits including fineness and maturity,etc., was performed using the Clusters of orthologous groups(COG), Gene ontology(GO), and Kyoto encyclopedia of genes and genomes(KEGG) databases to annotate QTLs for gene function. [Result] A total of 157 QTLs related to fiber quality were obtained and distributed on 20 chromosomes. QTLs with more traits on A03, A04, D02, A11 and D07 chromosomes clustered and may be the key chromosomes controlling fiber quality traits. A total of 13 stable QTLs were obtained, of which qFL-A03-1 and qFin-A11-4 were repeated in three environments, and nine other QTLs were repeated in two environments. And 4 763 candidate genes were annotated, with 2 416, 4 188, and 2 512 genes being annotated in COG, GO, and KEGG, respectively.Among them, 429 genes were annotated in stable QTLs. Some of these genes may be closely related to fiber quality.[Conclusion] The high-density genetic map obtained by high-throughput sequencing can help to obtain more QTLs, which is beneficial to the screening of candidate genes related to fiber quality and the improvement of fiber traits, and improves the breeding efficiency.
[Objective] This article aims to provide a theoretical basis for molecular marker-assisted breeding by quantitative trait loci(QTLs) mapping and gene function annotation of fiber quality. [Method] F2 populations were constructed using the two cotton cultivars(lines), CCRI 49 and 396289, as parents. Based on high-density genetic maps, the F2:3 families with three environments were included in the F2 population. The QTL mapping of seven fiber quality traits including fineness and maturity,etc., was performed using the Clusters of orthologous groups(COG), Gene ontology(GO), and Kyoto encyclopedia of genes and genomes(KEGG) databases to annotate QTLs for gene function. [Result] A total of 157 QTLs related to fiber quality were obtained and distributed on 20 chromosomes. QTLs with more traits on A03, A04, D02, A11 and D07 chromosomes clustered and may be the key chromosomes controlling fiber quality traits. A total of 13 stable QTLs were obtained, of which qFL-A03-1 and qFin-A11-4 were repeated in three environments, and nine other QTLs were repeated in two environments. And 4 763 candidate genes were annotated, with 2 416, 4 188, and 2 512 genes being annotated in COG, GO, and KEGG, respectively.Among them, 429 genes were annotated in stable QTLs. Some of these genes may be closely related to fiber quality.[Conclusion] The high-density genetic map obtained by high-throughput sequencing can help to obtain more QTLs, which is beneficial to the screening of candidate genes related to fiber quality and the improvement of fiber traits, and improves the breeding efficiency.
引文
[1] Chen Z J, Scheffler B E, Dennis E, et al. Toward sequencing cotton(Gossypium)genomes[J]. Plant Physiology, 2007, 145(4):1303-1310. https://doi.org/10.1104/pp.107.107672
[2]张震.陆地棉SNP遗传图谱构建及产量纤维品质性状的QTL定位[D].北京:中国农业科学院, 2015.Zhang Zhen. Construction of genetic maps of SNP in upland cotton and QTL mapping of yield fiber quality traits[D]. Beijing:Chinese Academy of Agricultural Sciences, 2015.
[3]陈利,张正圣,胡美纯,等.陆地棉遗传图谱构建及产量和纤维品质性状QTL定位[J].作物学报, 2008, 34(7):1199-1205.Chen Li, Zhang Zhengsheng, Hu Meichun, et al. Construction of genetic maps and QTL mapping of yield and fiber quality traits in upland cotton[J]. Acta Agronomica Sinica, 2008, 34(7):1199-1205.
[4]王琳,刘方,黎绍惠,等.鲁棉研15号纤维品质性状QTL定位研究[J].棉花学报, 2012, 24(2):97-105.Wang Lin, Liu Fang, Li Shaohui, et al. QTL mapping of fiber quality traits in Lumianyan 15[J]. Cotton Science, 2012, 24(2):97-105.
[5] Sun F D, Zhang J H, Wang S F, et al. QTL mapping for fiber quality traits across multiple generations and environments in upland cotton[J]. Molecular Breeding, 2012, 30(1):569-582.https://doi.org/10.1007/s11032-011-9645-z
[6] Zhang K, Zhang J, Ma J, et al. Genetic mapping and quantitative trait locus analysis of fiber quality traits using a three-parent composite population in upland cotton(Gossypium hirsutum L.)[J]. Molecular Breeding, 2012, 29(2):335-348. https://doi.org/10.1007/s11032-011-9549-y
[7] Liang Q Z, Cheng H, Hua H, et al. Construction of a linkage map and QTL mapping for fiber quality traits in upland cotton(Gossypium hirsutum L.)[J]. Science Bulletin, 2013, 58(26):3233-3243. https://doi.org/10.1007/s11434-013-5807-1
[8] Shao Q, Zhang F, Tang S, et al. Identifying QTL for fiber quality traits with three upland cotton(Gossypium hirsutum L.)populations[J]. Euphytica, 2014, 198(1):43-58. https://doi.org/10.1007/s10681-014-1082-8
[9] Tang S, Teng Z, Zhai T, et al. Construction of genetic map and QTL analysis of fiber quality traits for upland cotton(Gossypium hirsutum L.)[J]. Euphytica, 2015, 201(2):195-213. https://doi.org/10.1007/s10681-014-1189-y
[10] Cho R J, Mindrinos M, Richards D R, et al. Genome-wide mapping with biallelic markers in Arabidopsis thaliana[J]. Nature Genetics, 1999, 23(2):203-207. https://doi.org/10.1038/13833.
[11] Qi Z, Huang L, Zhu R, et al. A high-density genetic map for soybean based on specific length amplified fragment sequencing[J]. PLo S ONE, 2014, 9(8):e104871. https://doi.org/10.1371/journal.pone.0114349
[12] Wei Q, Wang Y, Qin X, et al. An SNP-based saturated genetic map and QTL analysis of fruit-related traits in cucumber using specific-length amplified fragment(SLAF)sequencing[J]. BMC Genomics, 2014, 15(1):1158. https://doi.org/10.1186/1471-2164-15-1158
[13] Zhang J, Zhang Q, Cheng T, et al. High-density genetic map construction and identification of a locus controlling weeping trait in an ornamental woody plant(Prunus mume Sieb. et Zucc)[J]. DNA Research, 2015, 22(3):183-191. https://doi.org/10.1093/dnares/dsv003
[14] Luo C, Shu B, Yao Q, et al. Construction of a high-density genetic map based on large-scale marker development in mango using specific-locus amplified fragment sequencing(SLAF-seq)[J]. Frontiers in Plant Science, 2016, 7:1310. https://doi.org/10.3389/fpls.2016.01310
[15] Zhang Z, Shang H H, Shi Y Z, et al. Construction of a high-density genetic map by specific locus amplified fragment sequencing(SLAF-seq)and its application to quantitative trait loci(QTL)analysis for boll weight in upland cotton(Gossypium hirsutum.)[J]. BMC Plant Biology, 2016, 16(1):79. https://doi.org/10.1186/s12870-016-0741-4
[16] Li F G, Fan G Y, Lu C R, et al. Genome sequence of cultivated upland cotton(Gossypium hirsutum TM-1)provides insights into genome evolution[J]. Nature Biotechnology, 2015, 33(5):524-530. https://doi.org/10.1038/nbt.3208
[17] Zhang T Z, Hu Y, Jiang W K, et al. Sequencing of allotetraploid cotton(Gossypium hirsutum L. acc. TM-1)provides a resource for fiber improvement[J]. Nature Biotechnology, 2015, 33(5):531-537. https://doi.org/10.1038/nbt.3207
[18] Darvasi A, Weinreb A, Minke V, et al. Detecting marker-QTL linkage and estimating QTL gene effect and map location using a saturated genetic map[J]. Genetics, 1993, 134(3):943-951.https://doi.org/10.1101/gad.7.7b.1459
[19]贾晓昀.陆地棉种内高密度遗传图谱构建及重要农艺性状QTL定位[D].杨凌:西北农林科技大学, 2017.Jia Xiaoyun. Construction of intraspecific high density genetic map and QTL mapping of important agronomic characters in upland cotton[D]. Yangling:Northwest A&F University, 2017.
[20]潘兆娥,胡希远,贾银华,等.棉花主要性状QTL定位的研究进展[J].安徽农业科学, 2010, 38(5):2325-2327.Pan Zhao’e, Hu Xiyuan, Jia Yinhua, et al. Research progress of QTL mapping for major traits in cotton[J]. Journal of Anhui Agricultural Sciences, 2010, 38(5):2325-2327.
[21]乔文青.陆地棉株高与纤维品质QTL定位及亲本抗盐性探讨[D].北京:中国农业科学院, 2018.Qiao Wenqing. QTL mapping of plant height and fiber quality in upland cotton and explore the salt resistance of parents[D].Beijing:Chinese Academy of Agricultural Sciences, 2015.
[22]宋国立,崔荣霞,王坤波,等.改良CTAB法快速提取棉花DNA[J].棉花学报, 1998, 10(5):273-275.Song Guoli, Cui Rongxia, Wang Kunbo, etal. A rapid improved CTAB method for extraction of cotton genomic DNA[J]. Cotton Science, 1998, 10(5):273-275.
[23] Sun X, Liu D, Zhang X, et al. SLAF-seq:An efficient method of large-Scale de novo SNP discovery and genotyping using high-throughput sequencing[J]. PLoS One, 2013, 8(3):e58700.https://doi.org/10.1371/journal.pone.0058700
[24] Li R, Li Y, Kristiansen K, et al. SOAP:short oligonucleotide alignment program[J]. Bioinformatics, 2008, 24(5):713-714.https://doi.org/10.1093/bioinformatics/btn025
[25] Stuber CW, Edwards MD, Wendel JF. Molecular marker-facilitated investigations of quantitative trait loci in maize. II. factors influencing yield and its component traits[J]. Crop Science,1987, 27(4):639-648. https://doi.org/10.2135/cropsci1987.0011183X002700040006x
[26]王寒涛.陆地棉遗传图谱的构建及其重要农艺性状的QTL定位[D].武汉:华中农业大学, 2015.Wang Hantao. Construction of genetic map of upland cotton and QTL mapping of its important agronomic traits[D]. Wuhan:Huazhong Agricultural University, 2015.
[27] He D H, Lin Z X, Zhang X L, et al. QTL mapping for economic traits based on a dense genetic map of cotton with PCR-based markers using the interspecific cross of Gossypium hirsutum×Gossypium barbadense[J]. Euphytica, 2007, 153(1/2):181-197.https://doi.org/10.1007/s10681-006-9254-9
[28]秦永生,叶文雪,刘任重,等.陆地棉纤维品质相关QTL定位研究[J].中国农业科学, 2009, 42(12):4145-4154.Qin Yongsheng, Ye Wenxue, Liu Renzhong, et al. QTL mapping of fiber quality in upland cotton[J]. Chinese Journal of Agricultural Sciences, 2009, 42(12):4145-4154.
[29] Qin Y M, Zhu Y X. How cotton fibers elongate:a tale of linear cell-growth mode[J]. Current Opinion in Plant Biology, 2011,14(1):106-111. https://doi.org/10.1016/j.pbi.2010.09.010
[30] Tang W, Tu L, Yang X, et al. The calcium sensor Gh Ca M7 promotes cotton fiber elongation by modulating reactive oxygen species(ROS)production[J]. New Phytologist, 2014, 202(2):509-520. https://doi.org/10.1111/nph.12676
[31] Tu L L, Zhang X L, Liang S G, et al. Genes expression analyses of sea-island cotton(Gossypium barbadense L.)during fiber development[J]. Plant Cell Reports, 2007, 26(8):1309-1320.https://doi.org/10.1007/s00299-007-0337-4
[32] Li P T, Wang M, Lu Q W, et al. Comparative transcriptome analysis of cotton fiber development of upland cotton(Gossypium hirsutum)and chromosome segment substitution lines from G. hirsutum×G. barbadense[J]. BMC Genomics, 2017, 18(1):705. https://doi.org/10.1186/s12864-017-4077-8
[33] Ji S J, Lu Y C, Feng J X, et al. Isolation and analyses of genes preferentially expressed during early cotton fiber development by subtractive PCR and c DNA array[J]. Nucleic Acids Research, 2003, 31(10):2534-2543. https://doi.org/10.1093/nar/gkg358
[34]南文智,吴嫚,于霁雯,等.利用高通量测序技术鉴定棉纤维发育相关miRNAs及其靶基因[J].棉花学报, 2013, 25(4):300-308.Nan Wenzhi, Wu Man, Yu Jiwen, et al. Identification of cotton fibrous development related miRNAs and their target genes using high-throughput sequencing technology[J]. Cotton Science,2013, 25(4):300-308.
[2]张震.陆地棉SNP遗传图谱构建及产量纤维品质性状的QTL定位[D].北京:中国农业科学院, 2015.Zhang Zhen. Construction of genetic maps of SNP in upland cotton and QTL mapping of yield fiber quality traits[D]. Beijing:Chinese Academy of Agricultural Sciences, 2015.
[3]陈利,张正圣,胡美纯,等.陆地棉遗传图谱构建及产量和纤维品质性状QTL定位[J].作物学报, 2008, 34(7):1199-1205.Chen Li, Zhang Zhengsheng, Hu Meichun, et al. Construction of genetic maps and QTL mapping of yield and fiber quality traits in upland cotton[J]. Acta Agronomica Sinica, 2008, 34(7):1199-1205.
[4]王琳,刘方,黎绍惠,等.鲁棉研15号纤维品质性状QTL定位研究[J].棉花学报, 2012, 24(2):97-105.Wang Lin, Liu Fang, Li Shaohui, et al. QTL mapping of fiber quality traits in Lumianyan 15[J]. Cotton Science, 2012, 24(2):97-105.
[5] Sun F D, Zhang J H, Wang S F, et al. QTL mapping for fiber quality traits across multiple generations and environments in upland cotton[J]. Molecular Breeding, 2012, 30(1):569-582.https://doi.org/10.1007/s11032-011-9645-z
[6] Zhang K, Zhang J, Ma J, et al. Genetic mapping and quantitative trait locus analysis of fiber quality traits using a three-parent composite population in upland cotton(Gossypium hirsutum L.)[J]. Molecular Breeding, 2012, 29(2):335-348. https://doi.org/10.1007/s11032-011-9549-y
[7] Liang Q Z, Cheng H, Hua H, et al. Construction of a linkage map and QTL mapping for fiber quality traits in upland cotton(Gossypium hirsutum L.)[J]. Science Bulletin, 2013, 58(26):3233-3243. https://doi.org/10.1007/s11434-013-5807-1
[8] Shao Q, Zhang F, Tang S, et al. Identifying QTL for fiber quality traits with three upland cotton(Gossypium hirsutum L.)populations[J]. Euphytica, 2014, 198(1):43-58. https://doi.org/10.1007/s10681-014-1082-8
[9] Tang S, Teng Z, Zhai T, et al. Construction of genetic map and QTL analysis of fiber quality traits for upland cotton(Gossypium hirsutum L.)[J]. Euphytica, 2015, 201(2):195-213. https://doi.org/10.1007/s10681-014-1189-y
[10] Cho R J, Mindrinos M, Richards D R, et al. Genome-wide mapping with biallelic markers in Arabidopsis thaliana[J]. Nature Genetics, 1999, 23(2):203-207. https://doi.org/10.1038/13833.
[11] Qi Z, Huang L, Zhu R, et al. A high-density genetic map for soybean based on specific length amplified fragment sequencing[J]. PLo S ONE, 2014, 9(8):e104871. https://doi.org/10.1371/journal.pone.0114349
[12] Wei Q, Wang Y, Qin X, et al. An SNP-based saturated genetic map and QTL analysis of fruit-related traits in cucumber using specific-length amplified fragment(SLAF)sequencing[J]. BMC Genomics, 2014, 15(1):1158. https://doi.org/10.1186/1471-2164-15-1158
[13] Zhang J, Zhang Q, Cheng T, et al. High-density genetic map construction and identification of a locus controlling weeping trait in an ornamental woody plant(Prunus mume Sieb. et Zucc)[J]. DNA Research, 2015, 22(3):183-191. https://doi.org/10.1093/dnares/dsv003
[14] Luo C, Shu B, Yao Q, et al. Construction of a high-density genetic map based on large-scale marker development in mango using specific-locus amplified fragment sequencing(SLAF-seq)[J]. Frontiers in Plant Science, 2016, 7:1310. https://doi.org/10.3389/fpls.2016.01310
[15] Zhang Z, Shang H H, Shi Y Z, et al. Construction of a high-density genetic map by specific locus amplified fragment sequencing(SLAF-seq)and its application to quantitative trait loci(QTL)analysis for boll weight in upland cotton(Gossypium hirsutum.)[J]. BMC Plant Biology, 2016, 16(1):79. https://doi.org/10.1186/s12870-016-0741-4
[16] Li F G, Fan G Y, Lu C R, et al. Genome sequence of cultivated upland cotton(Gossypium hirsutum TM-1)provides insights into genome evolution[J]. Nature Biotechnology, 2015, 33(5):524-530. https://doi.org/10.1038/nbt.3208
[17] Zhang T Z, Hu Y, Jiang W K, et al. Sequencing of allotetraploid cotton(Gossypium hirsutum L. acc. TM-1)provides a resource for fiber improvement[J]. Nature Biotechnology, 2015, 33(5):531-537. https://doi.org/10.1038/nbt.3207
[18] Darvasi A, Weinreb A, Minke V, et al. Detecting marker-QTL linkage and estimating QTL gene effect and map location using a saturated genetic map[J]. Genetics, 1993, 134(3):943-951.https://doi.org/10.1101/gad.7.7b.1459
[19]贾晓昀.陆地棉种内高密度遗传图谱构建及重要农艺性状QTL定位[D].杨凌:西北农林科技大学, 2017.Jia Xiaoyun. Construction of intraspecific high density genetic map and QTL mapping of important agronomic characters in upland cotton[D]. Yangling:Northwest A&F University, 2017.
[20]潘兆娥,胡希远,贾银华,等.棉花主要性状QTL定位的研究进展[J].安徽农业科学, 2010, 38(5):2325-2327.Pan Zhao’e, Hu Xiyuan, Jia Yinhua, et al. Research progress of QTL mapping for major traits in cotton[J]. Journal of Anhui Agricultural Sciences, 2010, 38(5):2325-2327.
[21]乔文青.陆地棉株高与纤维品质QTL定位及亲本抗盐性探讨[D].北京:中国农业科学院, 2018.Qiao Wenqing. QTL mapping of plant height and fiber quality in upland cotton and explore the salt resistance of parents[D].Beijing:Chinese Academy of Agricultural Sciences, 2015.
[22]宋国立,崔荣霞,王坤波,等.改良CTAB法快速提取棉花DNA[J].棉花学报, 1998, 10(5):273-275.Song Guoli, Cui Rongxia, Wang Kunbo, etal. A rapid improved CTAB method for extraction of cotton genomic DNA[J]. Cotton Science, 1998, 10(5):273-275.
[23] Sun X, Liu D, Zhang X, et al. SLAF-seq:An efficient method of large-Scale de novo SNP discovery and genotyping using high-throughput sequencing[J]. PLoS One, 2013, 8(3):e58700.https://doi.org/10.1371/journal.pone.0058700
[24] Li R, Li Y, Kristiansen K, et al. SOAP:short oligonucleotide alignment program[J]. Bioinformatics, 2008, 24(5):713-714.https://doi.org/10.1093/bioinformatics/btn025
[25] Stuber CW, Edwards MD, Wendel JF. Molecular marker-facilitated investigations of quantitative trait loci in maize. II. factors influencing yield and its component traits[J]. Crop Science,1987, 27(4):639-648. https://doi.org/10.2135/cropsci1987.0011183X002700040006x
[26]王寒涛.陆地棉遗传图谱的构建及其重要农艺性状的QTL定位[D].武汉:华中农业大学, 2015.Wang Hantao. Construction of genetic map of upland cotton and QTL mapping of its important agronomic traits[D]. Wuhan:Huazhong Agricultural University, 2015.
[27] He D H, Lin Z X, Zhang X L, et al. QTL mapping for economic traits based on a dense genetic map of cotton with PCR-based markers using the interspecific cross of Gossypium hirsutum×Gossypium barbadense[J]. Euphytica, 2007, 153(1/2):181-197.https://doi.org/10.1007/s10681-006-9254-9
[28]秦永生,叶文雪,刘任重,等.陆地棉纤维品质相关QTL定位研究[J].中国农业科学, 2009, 42(12):4145-4154.Qin Yongsheng, Ye Wenxue, Liu Renzhong, et al. QTL mapping of fiber quality in upland cotton[J]. Chinese Journal of Agricultural Sciences, 2009, 42(12):4145-4154.
[29] Qin Y M, Zhu Y X. How cotton fibers elongate:a tale of linear cell-growth mode[J]. Current Opinion in Plant Biology, 2011,14(1):106-111. https://doi.org/10.1016/j.pbi.2010.09.010
[30] Tang W, Tu L, Yang X, et al. The calcium sensor Gh Ca M7 promotes cotton fiber elongation by modulating reactive oxygen species(ROS)production[J]. New Phytologist, 2014, 202(2):509-520. https://doi.org/10.1111/nph.12676
[31] Tu L L, Zhang X L, Liang S G, et al. Genes expression analyses of sea-island cotton(Gossypium barbadense L.)during fiber development[J]. Plant Cell Reports, 2007, 26(8):1309-1320.https://doi.org/10.1007/s00299-007-0337-4
[32] Li P T, Wang M, Lu Q W, et al. Comparative transcriptome analysis of cotton fiber development of upland cotton(Gossypium hirsutum)and chromosome segment substitution lines from G. hirsutum×G. barbadense[J]. BMC Genomics, 2017, 18(1):705. https://doi.org/10.1186/s12864-017-4077-8
[33] Ji S J, Lu Y C, Feng J X, et al. Isolation and analyses of genes preferentially expressed during early cotton fiber development by subtractive PCR and c DNA array[J]. Nucleic Acids Research, 2003, 31(10):2534-2543. https://doi.org/10.1093/nar/gkg358
[34]南文智,吴嫚,于霁雯,等.利用高通量测序技术鉴定棉纤维发育相关miRNAs及其靶基因[J].棉花学报, 2013, 25(4):300-308.Nan Wenzhi, Wu Man, Yu Jiwen, et al. Identification of cotton fibrous development related miRNAs and their target genes using high-throughput sequencing technology[J]. Cotton Science,2013, 25(4):300-308.