水稻耐淹成苗率相关性状全基因组的关联分析
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摘要
【背景】耐淹成苗率低是限制直播稻产量的重要因素,挖掘高种子活力、低氧萌发能力强的水稻材料是提高耐淹成苗率的关键,但控制耐淹成苗率的遗传位点的挖掘仍然比较有限。【目的】利用来源广泛的自然种质,分析影响耐淹成苗率的关键表型性状,挖掘相关的遗传位点和候选基因,为直播稻耐淹成苗机理研究提供一定的理论和材料基础。【方法】以200份来源广泛的水稻种质为材料,在有氧环境下进行发芽试验,测量种子发芽率、发芽指数和活力指数;在低氧条件下测量芽鞘长和芽鞘直径;进行耐淹成苗试验,水深10 cm,20 d后测量耐淹成苗率。分析各性状间的相关性,挖掘影响耐淹成苗率的关键性状;利用简化基因组测序对以上6个表型进行全基因组关联分析,鉴定与性状显著关联的SNP位点,并在关联区间内筛选候选基因;对02428和YZX 2份材料进行有氧、无氧以及氧气含量转换条件下的转录组检测,结合全基因组关联分析结果,分析候选基因的表达模式差异。【结果】种子活力、芽鞘表型和耐淹成苗率在200份材料间存在广泛的遗传变异,其中,芽鞘长和活力指数的变异系数最大;相关分析结果表明,芽鞘长、活力指数与耐淹成苗率呈极显著正相关;通过全基因组关联分析,共鉴定出8个与活力指数显著关联的位点,15个与芽鞘长显著关联的位点;结合基因组注释,在关联区间筛选出6个与活力指数相关的候选基因,7个与芽鞘长度相关的候选基因;进一步比较13个基因在有氧、无氧及氧气转换条件下的表达模式以及表达量的变化,发现Os02g0657000、Os03g0592500、Os08g0380100表达量变化显著,表现出对氧气处理的敏感性。【结论】种子活力、芽鞘长与耐淹成苗率密切相关,可作为筛选高耐淹成苗水稻材料的重要性状。全基因组关联分析、转录组分析与基因表达模式比较的联合应用可提高候选基因的筛选效率。水稻耐淹成苗过程可能受到与逆境胁迫、光合作用相关基因的调控。
【Background】 The low seedling rate of direct seeding rice is an important factor limiting its yield. Mining rice materials with high seed viability and low oxygen germination ability is the key to improving the seedling rate and solving the problem of seedlings in direct seeding rice. 【Objective】 The key phenotypic traits affecting the rate of emergence and tolerance of seedlings were analyzed, and the relevant genetic loci and candidate genes were mined to provide a theoretical and material basis for the study of direct seeding rice cultivars and the mechanism of resistance to flooding. 【Method】 Using 200 rice germplasms from a wide range of sources. The germination test was carried out in an aerobic environment, and the seed viability phenotype was measured including germination rate, germination index and viability index; The coleoptile length and coleoptile diameter were measured under hypoxic conditions. The flood-tolerant seedling experiment was carried out, the water depth was 10 cm, and the flood-tolerant seedling rate was measured after 20 d. The correlation between various traits was analyzed, and the key traits affecting the rate of tolerance to flooding were explored. Genome-wide association analysis was performed on the above six phenotypes by simplified genome sequencing, and SNP sites significantly associated with traits were identified and within the correlation interval. Screening candidate genes related to the research purpose; transcriptome detection under the conditions of aerobic, anaerobic and oxygen content conversion of 02428 and YZX two materials, combined with genome-wide association analysis results, analysis of differences in expression patterns of candidate genes. 【Result】 Seed viability, coleoptile phenotype and seedling rate showed extensive genetic variation among 200 materials. Among them, the variation of coleoptile length and viability index was the most abundant, and the coefficient of variation was the largest. At the same time, the results of correlation analysis showed that there was a significant positive correlation between the coleoptile length, viability index and the seedling rate. Through genome-wide association analysis, 8 sites significantly associated with the viability index and 15 sites significantly associated with the coleoptile length were identified. Based on the correlation of seed growth and development and stress resistance, six candidate genes related to viability index and seven candidate genes related to the coleoptile length were screened in the relevant interval. Further comparison of 13 genes in aerobic and anaerobic the expression patterns and expression changes under oxygen conversion conditions showed that the three genes Os02g0657000, Os03g0592500 and Os08g0380100 showed different expression patterns when the oxygen content changed, and the expression amount changed significantly, showing sensitivity to oxygen treatment. 【Conclusion】 Seed viability and coleoptile length were closely related to the rate of flooding and seedling emergence, which could be used as an important trait for screening flood-tolerant rice materials. Combining genome-wide association analysis, transcriptome analysis and gene expression pattern can improve the screening efficiency of candidate genes for hypoxia tolerance germination of rice seeds; flooding tolerance of rice seedlings may be regulated by genes related to stress and photosynthesis.
【Background】 The low seedling rate of direct seeding rice is an important factor limiting its yield. Mining rice materials with high seed viability and low oxygen germination ability is the key to improving the seedling rate and solving the problem of seedlings in direct seeding rice. 【Objective】 The key phenotypic traits affecting the rate of emergence and tolerance of seedlings were analyzed, and the relevant genetic loci and candidate genes were mined to provide a theoretical and material basis for the study of direct seeding rice cultivars and the mechanism of resistance to flooding. 【Method】 Using 200 rice germplasms from a wide range of sources. The germination test was carried out in an aerobic environment, and the seed viability phenotype was measured including germination rate, germination index and viability index; The coleoptile length and coleoptile diameter were measured under hypoxic conditions. The flood-tolerant seedling experiment was carried out, the water depth was 10 cm, and the flood-tolerant seedling rate was measured after 20 d. The correlation between various traits was analyzed, and the key traits affecting the rate of tolerance to flooding were explored. Genome-wide association analysis was performed on the above six phenotypes by simplified genome sequencing, and SNP sites significantly associated with traits were identified and within the correlation interval. Screening candidate genes related to the research purpose; transcriptome detection under the conditions of aerobic, anaerobic and oxygen content conversion of 02428 and YZX two materials, combined with genome-wide association analysis results, analysis of differences in expression patterns of candidate genes. 【Result】 Seed viability, coleoptile phenotype and seedling rate showed extensive genetic variation among 200 materials. Among them, the variation of coleoptile length and viability index was the most abundant, and the coefficient of variation was the largest. At the same time, the results of correlation analysis showed that there was a significant positive correlation between the coleoptile length, viability index and the seedling rate. Through genome-wide association analysis, 8 sites significantly associated with the viability index and 15 sites significantly associated with the coleoptile length were identified. Based on the correlation of seed growth and development and stress resistance, six candidate genes related to viability index and seven candidate genes related to the coleoptile length were screened in the relevant interval. Further comparison of 13 genes in aerobic and anaerobic the expression patterns and expression changes under oxygen conversion conditions showed that the three genes Os02g0657000, Os03g0592500 and Os08g0380100 showed different expression patterns when the oxygen content changed, and the expression amount changed significantly, showing sensitivity to oxygen treatment. 【Conclusion】 Seed viability and coleoptile length were closely related to the rate of flooding and seedling emergence, which could be used as an important trait for screening flood-tolerant rice materials. Combining genome-wide association analysis, transcriptome analysis and gene expression pattern can improve the screening efficiency of candidate genes for hypoxia tolerance germination of rice seeds; flooding tolerance of rice seedlings may be regulated by genes related to stress and photosynthesis.
引文
[1]刘贵富,陈明江,李明,吕慧颖,葛毅强,魏珣,杨维才.水稻育种行业创新进展.植物遗传资源学报,2018,19(3):416-429.LIU G F,CHEN M J,LI M,LU H Y,GE Y Q,WEI X,YANG W C.Innovation progress in rice breeding industry.Journal of Plant Genetic Resources,2018,19(3):416-429.(in Chinese)
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[4]YAMAUCHI M,BISWAS J K.Rice cultivar difference in seedling establishment in flooded soil.Plant&Soil,1997,189(1):145-153.
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[6]SEPTININGSIH E M,SENDON P M D,SANCHEZ D L,ISMAILA M,MACKILL D J.QTL mapping and confirmation for tolerance of anaerobic conditions during germination derived from the rice landrace Ma-Zhan Red.Theoretical and Applied Genetics,2013,126(5):1357-1366.
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[18]BI F C,ZHANG Q F,LIU Z,FANG C,LI J,SU J B,GREENBERGJ T,WANG H B,YAO N.A conserved cysteine motif is critical for rice ceramide kinase activity and function.PLoS ONE,2011,6(3):e18079.
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[23]ZENG L R,QU S,BORDEOS A,YANG C,BARAOIDAN M,YANH,XIE Q,NAHM B H,LEUNG H,WANG G L.Spotted leaf11,a negative regulator of plant cell death and defense,encodes a U-box/armadillo repeat protein endowed with E3 ubiquitin ligase activity.The Plant Cell,2004,16(10):2795-2808.
[24]LIANG Y,ZHAO X,JONES A M,GAO Y.G proteins sculp root architecture in response to nitrogen in rice and Arabidopsis.Plant Science,2018,274:129-136.
[25]SINGH G,SARKAR N K,GROVER A.Mapping of domains of heat stress transcription factor OsHsfA6a responsible for its transactivation activity.Plant Science,2018,274:80-90.
[26]ZHU S,GAO F,CAO X,CHEN M,YE G,WEI C,LI Y.The rice dwarf virus P2 protein interacts with ent-kaurene oxidases in vivo,leading to reduced biosynthesis of gibberellins and rice dwarf symptoms.Plant Physiology,2005,139(4):1935-1945.
[27]YONG H C,KIM C Y,MIN C K,KIM C Y,KIM M C,KIM I H,PARK C Y,KIM J C,PARK B O,KOO S C,YOON H W,CHUNG WS,LIM C O,LEE S Y,CHO M J.BWMK1,a rice mitogen-activated protein kinase,locates in the nucleus and mediates pathogenesisrelated gene expression by activation of a transcription factor.Plant Physiology,2003,132(4):1961-1972.
[28]ZHONG R,CUI D,PHILLIPS D R,YE Z H.A novel rice xylosyltransferase catalyzes the addition of 2-o-xylosyl side chains onto the xylan backbone.Plant&Cell Physiology,2018,59(3):554.
[29]CHEUNG M Y,XUE Y,ZHOU L,LI M W,SUN S S,LAM H M.An ancient P-loop GTPase in rice is regulated by a higher plant-specific regulatory protein.Journal of Biological Chemistry,2010,285(48):37359-37369.
[30]蒋彭炎.直播稻的生育特点和增产对策.中国稻米,1996(4):30-33.JIANG P Y.Fertility characteristics and yield increase strategies of direct seeding rice.China Rice,1996(4):30-33.(in Chinese)
[31]侯名语,江玲,王春明,万建民.水稻种子低氧发芽力的QTL定位和上位性分析.中国水稻科学,2004,18(6):483-488.HOU M Y,JIANG L,WANG C M,WAN J M.QTL mapping and epistasis analysis of hypoxia germination of rice seeds.Chinese Journal of Rice Science,2004,18(6):483-488.(in Chinese)
[32]ANGAJI S A,SEPTININGSIH E M,MACKILL D J,ISMAIL A M.QTLs associated with tolerance of flooding during germination in rice(Oryza sativa L.).Euphytica,2010,172(2):159-168.
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[2]章孟臣.水稻耐淹发芽相关性状的全基因组关联分析[D].北京:中国农业科学院,2016.ZHANG M C.Genome-wide association analysis of traits related to flooding and germination in rice[D].Beijing:Chinese Academy of Agricultural Sciences,2016.(in Chinese)
[3]YAMAUCHI M,AGUILAR A M,VAUGHAN D A,SESHU D V.Rice(Oryza sativa L.)germplasm suitable for direct sowing under flooded soil surface.Euphytica,1993,67(3):177-184.
[4]YAMAUCHI M,BISWAS J K.Rice cultivar difference in seedling establishment in flooded soil.Plant&Soil,1997,189(1):145-153.
[5]陈孙禄,王俊敏,潘佑找,马健阳,张建辉,张红生,滕胜.水稻萌发耐淹性的遗传分析.植物学报,2012,47(1):28-35.CHEN S L,WANG J M,PAN Y Z,MA J Y,ZHANG J H,ZHANG HS,TENG S.Genetic analysis of rice germination tolerance to flooding.Acta Botanica Sinica,2012,47(1):28-35.(in Chinese)
[6]SEPTININGSIH E M,SENDON P M D,SANCHEZ D L,ISMAILA M,MACKILL D J.QTL mapping and confirmation for tolerance of anaerobic conditions during germination derived from the rice landrace Ma-Zhan Red.Theoretical and Applied Genetics,2013,126(5):1357-1366.
[7]LEE H S,SASAKI K,KANG J W,SATO T,SONG W Y,AHN S N.Mesocotyl elongation is essential for seedling emergence under deep-seeding condition in rice.Rice,2017,10(1):32.
[8]MACKAY I,POWELL W.Methods for linkage disequilibrium mapping in crops.Trends in Plant Science,2007,12(2):57-63.
[9]MACKAY T F C,STONE E A,AYROLES J F.The genetics of quantitative traits:Challenges and prospects.Nature Reviews Genetics,2009,10(8):565-577.
[10]BAI X,ZHAO H,HUANG Y,XIE W B,HAN Z M,ZHANG B,GUO Z L,YANG L,DONG H J,XUE W Y,LI G W,HU G,HU Y,XING Y Z.Genome-wide association analysis reveals different genetic control in panicle architecture between and rice.Plant Genome,2016,9(2).
[11]HAN Z,ZHANG B,ZHAO H,AYAAD M,XING Y Z.Genome-wide association studies reveal that diverse heading date genes respond to short and long day lengths between indica and japonica rice.Frontiers in Plant Science,2016,7:1270.
[12]MAGWA R A,ZHAO H,XING Y.Genome-wide association mapping revealed a diverse genetic basis of seed dormancy across subpopulations in rice(Oryza sativa L.).BMC Genetics,2016,17(1):28.
[13]MAGWA R A,ZHAO H,YAO W,XIE W,YANG L,BAIX.Genomewide association analysis for awn length linked to the seed shattering gene qSH1 in rice.Journal of Genetics,2016,95(3):1-8.
[14]ZHOU P B,XIE W B,HUSSIAN S,LI Y,XIA D,ZHAO H,SUN S,CHEN J,YE H,HOU J,ZHAO D,GAO G,ZHANG Q,WANG G,LIAN X,XIAO J,YU S,LI X,HE Y.Genome-wide association analyses reveal the genetic basis of stigma exsertion in rice.Molecular Plant,2017,10(4):634-644.
[15]王洋.适于直播的水稻种质资源筛选及种子活力和幼苗耐缺氧能力优异等位变异的发掘[D].南京:南京农业大学,2009.WANG Y.Screening of rice germplasm resources suitable for direct seeding and excavation of seed vigor and excellent allergic variation of seedling tolerance to hypoxia[D].Nanjing:Nanjing Agricultural University,2009.(in Chinese)
[16]HSU S K,TUNG C W.Genetic mapping of anaerobic germinationassociated QTLs controlling coleoptile elongation in rice.Rice,2015,8(1):1-12.
[17]LEE K W,CHEN P W,LU C A,CHEN S,HO Y H,YU S M.Coordinated responses to oxygen and sugar deficiency allow rice seedlings to tolerate flooding.Science Signaling,2009,2(91):ra61.
[18]BI F C,ZHANG Q F,LIU Z,FANG C,LI J,SU J B,GREENBERGJ T,WANG H B,YAO N.A conserved cysteine motif is critical for rice ceramide kinase activity and function.PLoS ONE,2011,6(3):e18079.
[19]SUGIYAMA K,HAYAKAWA T,KUDO T,ITO T,YAMAYA T.Interaction of N-acetylglutamate kinase with a PII-like protein in rice.Plant&Cell Physiology,2004,45(12):1768-1778.
[20]MOEDER W,YOSHIOKA K.CNGCs break through-A rice cyclic nucleotide-gated channel paves the way for pollen tube growth.PLoSGenetics,2017,13(11):e1007066.
[21]MORI Y,YAMAMOTO T,SAKAGUCHI N,ISHIBASHI T,FURUKAWA T,KADOTA Y,KUCHITSU K,HASHIMOTO J,KIMURA S,SAKAGUCHI K.Characterization of the origin recognition complex(ORC)from a higher plant,rice(Oryza sativa L.).Gene,2005,353(1):23-30.
[22]MIYOSHI K,AHN B O,KAWAKATSU T,ITO Y,ITOH J,NAGATOY,KURATA N.PLASTOCHRON1,a timekeeper of leaf initiation in rice,encodes cytochrome P450.Proceedings of the National Academy of Sciences of the United States of America,2004,101(3):875-880.
[23]ZENG L R,QU S,BORDEOS A,YANG C,BARAOIDAN M,YANH,XIE Q,NAHM B H,LEUNG H,WANG G L.Spotted leaf11,a negative regulator of plant cell death and defense,encodes a U-box/armadillo repeat protein endowed with E3 ubiquitin ligase activity.The Plant Cell,2004,16(10):2795-2808.
[24]LIANG Y,ZHAO X,JONES A M,GAO Y.G proteins sculp root architecture in response to nitrogen in rice and Arabidopsis.Plant Science,2018,274:129-136.
[25]SINGH G,SARKAR N K,GROVER A.Mapping of domains of heat stress transcription factor OsHsfA6a responsible for its transactivation activity.Plant Science,2018,274:80-90.
[26]ZHU S,GAO F,CAO X,CHEN M,YE G,WEI C,LI Y.The rice dwarf virus P2 protein interacts with ent-kaurene oxidases in vivo,leading to reduced biosynthesis of gibberellins and rice dwarf symptoms.Plant Physiology,2005,139(4):1935-1945.
[27]YONG H C,KIM C Y,MIN C K,KIM C Y,KIM M C,KIM I H,PARK C Y,KIM J C,PARK B O,KOO S C,YOON H W,CHUNG WS,LIM C O,LEE S Y,CHO M J.BWMK1,a rice mitogen-activated protein kinase,locates in the nucleus and mediates pathogenesisrelated gene expression by activation of a transcription factor.Plant Physiology,2003,132(4):1961-1972.
[28]ZHONG R,CUI D,PHILLIPS D R,YE Z H.A novel rice xylosyltransferase catalyzes the addition of 2-o-xylosyl side chains onto the xylan backbone.Plant&Cell Physiology,2018,59(3):554.
[29]CHEUNG M Y,XUE Y,ZHOU L,LI M W,SUN S S,LAM H M.An ancient P-loop GTPase in rice is regulated by a higher plant-specific regulatory protein.Journal of Biological Chemistry,2010,285(48):37359-37369.
[30]蒋彭炎.直播稻的生育特点和增产对策.中国稻米,1996(4):30-33.JIANG P Y.Fertility characteristics and yield increase strategies of direct seeding rice.China Rice,1996(4):30-33.(in Chinese)
[31]侯名语,江玲,王春明,万建民.水稻种子低氧发芽力的QTL定位和上位性分析.中国水稻科学,2004,18(6):483-488.HOU M Y,JIANG L,WANG C M,WAN J M.QTL mapping and epistasis analysis of hypoxia germination of rice seeds.Chinese Journal of Rice Science,2004,18(6):483-488.(in Chinese)
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