Identification of QTLs with Additive, Epistatic, and QTL × Seed Maturity Interaction Effects for Seed Vigor in Rice
详细信息 查看全文
- 作者：Yanyan Lai ; Jinping Cheng ; Yongqi He ; Bin Yang…
- 关键词：Rice ; Seed vigor ; Seed maturity ; Quantitative trait loci ; Elite allele
- 刊名：Plant Molecular Biology Reporter
- 出版年：2016
- 出版时间：February 2016
- 年：2016
- 卷：34
- 期：1
- 页码：160-171
- 全文大小：1,261 KB
- 参考文献：Bethke PC, Libourel IG, Aoyama N, Chung YY, Still DW, Jones RL (2007) The Arabidopsis aleurone layer responds to nitric oxide, gibberellin, and abscisic acid and is sufficient and necessary for seed dormancy. Plant Physiol 143:1173–1188PubMedCentral CrossRef PubMed
Bewley DJ, Bradford K, Hillorst H, Nonogaki H (2013) Seeds: physiology of development, germination and dormancy, 3rd Edn. Springer
Catusse J, Job C, Job D (2008) Transcriptome- and proteome-wide analyses of seed germination. C R Biol 31:815–822CrossRef
Cheng X, Cheng J, Huang X, Lai Y, Wang L, Du W, Wang Z, Zhang H (2013) Dynamic quantitative trait loci analysis of seed reserve utilization during three germination stages in rice. PLoS One 8, e80002PubMedCentral CrossRef PubMed
Cheng J, Wang L, Du W, Lai Y, Huang X, Wang Z, Zhang H (2014) Dynamic quantitative trait locus analysis of seed dormancy at three development stages in rice. Mol Breed 34:501–510CrossRef
Fait A, Angelovici R, Less H, Ohad I, Urbanczyk-Wochniak E, Fernie AR, Galili G (2006) Arabidopsis seed development and germination is associated with temporally distinct metabolic switches. Plant Physiol 142:839–854PubMedCentral CrossRef PubMed
Fujino K, Sekiguchi H, Sato T, Kiuchi H, Nonoue Y, Takeuchi Y, Ando T, Lin SY, Yano M (2004) Mapping of quantitative trait loci controlling low-temperature germinability in rice (Oryza sativa L.). Theor Appl Genet 108:794–799CrossRef PubMed
Fujino K, Sekiguchi H, Matsuda Y, Sugimoto K, Ono K, Yano M (2008) Molecular identification of a major quantitative trait locus, qLTG3-1, controlling low temperature germinability in rice. Proc Natl Acad Sci U S A 105:12623–12628PubMedCentral CrossRef PubMed
Guan YJ, Hu J, Wang ZF, Zhu SJ, Wang JC, Knapp A (2013) Time series regression analysis between changes in kernel size and seed vigor during developmental stage of sh2 sweet corn (Zea mays L.) seeds. Sci Hortic 154:25–30CrossRef
Han LZ, Zhang YY, Qiao YL, Cao GL, Zhang SY, Kim JH, Koh HJ (2006) Genetic and QTL analysis for low-temperature vigor of germination in rice. Acta Genet Sin 33:998–1006CrossRef PubMed
Hayashi E, Aoyama N, Still DW (2008) Quantitative trait loci associated with lettuce seed germination under different temperature and light environments. Genome 51:928–947CrossRef PubMed
Huang D, Koh C, Feurtado JA, Tsang EW, Cutler AJ (2013) MicroRNAs and their putative targets in Brassica napus seed maturation. BMC Genomics 14:140PubMedCentral CrossRef PubMed
Ji SL, Jiang L, Wang YH, Zhang WW, Liu XL, Liu SJ, Chen LM, Zhai HQ, Wan JM (2009) Quantitative trait loci mapping and stability for low temperature germination ability of rice. Plant Breed 128:387–392CrossRef
Jiang L, Liu SJ, Hou MY, Tang JY, Chen LM, Zhai HQ, Wan JM (2006) Analysis of QTLs for seed low temperature germinability and anoxia germinability in rice (Oryza sativa L.). Field Crop Res 98:68–75CrossRef
Joosen RV, Kodde J, Willems LA, Ligterink W, van der Plas LH, Hilhorst HW (2010) GERMINATOR: a software package for high-throughput scoring and curve fitting of Arabidopsis seed germination. Plant J 62:148–159CrossRef PubMed
Marzougui S, Sugimoto K, Yamanouchi U, Shimono M, Hoshino T, Hori K, Kobayashi M, Ishiyama K, Yano M (2012) Mapping and characterization of seed dormancy QTLs using chromosome segment substitution lines in rice. Theor Appl Genet 124:893–902CrossRef PubMed
McCouch SR, CGSNL (Committee on Gene Symbolization, Nomenclature, Linkage, Rice Genetics Cooperative) (2008) Gene nomenclature system for rice. Rice 1:72–84CrossRef
Miura K, Lin Y, Yano M, Nagamine T (2002) Mapping quantitative trait loci controlling seed longevity in rice (Oryza sativa L.). Theor Appl Genet 104:981–986CrossRef PubMed
Niu Y, Xu Y, Liu XF, Yang SX, Wei SP, Xie FT, Zhang YM (2013) Association mapping for seed size and shape traits in soybean cultivars. Mol Breed 31:785–794CrossRef
Sugimoto K, Takeuchi Y, Ebana K, Miyao A, Hirochika H, Hara N, Ishiyama K, Kobayashi M, Ban Y, Hattori T, Yano M (2010) Molecular cloning of Sdr4, a regulator involved in seed dormancy and domestication of rice. Proc Natl Acad Sci U S A 107:5792–5797PubMedCentral CrossRef PubMed
Sun Q, Wang JH, Sun BQ (2007) Advances on seed vigor physiological and genetic mechanisms. Agric Sci China 6:1060–1066CrossRef
Sun Y, Wang J, Crouch JH, Xu Y (2010) Efficiency of selective genotyping for genetic analysis of complex traits and potential applications in crop improvement. Mol Breed 26:493–511CrossRef
Takai T, Fukuta Y, Shiraiwa T, Horie T (2005) Time-related mapping of quantitative trait loci controlling grain-filling in rice (Oryza sativa L.). J Exp Bot 56:2107–2118CrossRef PubMed
Venuprasad R, Dalid CO, Del Valle M, Zhao D, Espiritu M, Sta Cruz MT, Amante M, Kumar A, Atlin GN (2009) Identification and characterization of large-effect quantitative trait loci for grain yield under lowland drought stress in rice using bulk-segregant analysis. Theor Appl Genet 120:177–190CrossRef PubMed
Wang ZF, Wang JF, Bao YM, Wang FH, Zhang HS (2010) Quantitative trait loci analysis for rice seed vigor during the germination stage. J Zhejiang Univ Sci B 11:958–964PubMedCentral CrossRef PubMed
Wang Z, Wang J, Bao Y, Wu Y, Zhang H (2011) Quantitative trait loci controlling rice seed germination under salt stress. Euphytica 178:297–307CrossRef
Wang Z, Cheng J, Chen Z, Huang J, Bao Y, Wang J, Zhang H (2012) Identification of QTLs with main, epistatic and QTL × environment interaction effects for salt tolerance in rice seedlings under different salinity conditions. Theor Appl Genet 125:807–815CrossRef PubMed
Wang L, Cheng J, Lai Y, Du W, Huang X, Wang Z, Zhang H (2014) Identification of QTLs with additive, epistatic and QTL × development interaction effects for seed dormancy in rice. Planta 239:411–420CrossRef PubMed
Wu R, Lin M (2006) Functional mapping-how to map and study the genetic architecture of dynamic complex traits. Nat Rev Genet 7:229–237CrossRef PubMed
Xiao N, Huang WN, Li AH, Gao Y, Li YH, Pan CH, Ji H, Zhang XX, Dai Y, Dai ZY, Chen JM (2015) Fine mapping of the qLOP2 and qPSR2-1 loci associated with chilling stress tolerance of wild rice seedlings. Theor Appl Genet 128:173–185CrossRef PubMed
Xie L, Tan Z, Zhou Y, Xu R, Feng L, Xing Y, Qi X (2014) Identification and fine mapping of quantitative trait loci for seed vigor in germination and seedling establishment in rice. J Integr Plant Biol 56:749–759CrossRef PubMed
Yang J, Hu CC, Ye XZ, Zhu J (2005) QTLNetwork 2.0. http://ibi.zju.edu.cn/software/qtlnetwork
You J, Li Q, Yue B, Xue WY, Luo LJ, Xiong LZ (2006) Identification of quantitative trait loci for ABA sensitivity at seed germination and seedling stages in rice. Yi Chuan Xue Bao 33:532–541PubMed
Zhang ZH, Qu XS, Wan S, Chen LH, Zhu YG (2005) Comparison of QTL controlling seedling vigour under different temperature conditions using recombinant inbred lines in rice (Oryza sativa). Ann Bot 95:423–429PubMedCentral CrossRef PubMed
Zhu J (1995) Analysis of conditional genetic effects and variance components in developmental genetics. Genetics 141:1633–1639PubMedCentral PubMed - 作者单位：Yanyan Lai (1)
Jinping Cheng (1)
Yongqi He (1)
Bin Yang (1)
Zhoufei Wang (1)
Hongsheng Zhang (1)
1. The Laboratory of Seed Science and Technology, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, People’s Republic of China - 刊物类别：Biomedical and Life Sciences
- 刊物主题：Life Sciences
Plant Sciences
Plant Physiology - 出版者：Springer Netherlands
- ISSN：1572-9818
文摘
Seed maturity is a critical process of seed vigor establishment. In this study, one rice population of recombinant inbred lines (RILs) was used to determine the genetic characteristics of seed vigor, including the germination potential (GP), germination rate (GR), germination index (GI), and time for 50 % of germination (T50), at 4, 5, and 6 weeks after heading in 2 years. Significant differences of seed vigor were observed among two parents and RIL population; the heritability of four traits was more than 90 % at three maturity stages. A total of 19 additive and 2 epistatic quantitative trait loci (QTL) for seed vigor were identified using QTL Cartographer and QTLNetwork program, respectively, in 2012, while 16 simple sequence repeat (SSR) markers associated with seed vigor were detected using bulked segregant analysis (BSA) in 2013. The phenotypic variation explained by each additive, epistatic QTL, and QTL × seed maturity interaction ranged from 9.19 to 22.94 %, 7.23 to 7.75 %, and 0.05 to 0.63 %, respectively. Ten additive QTLs were stably expressed in 2 years which might play important roles in establishment of seed vigor in different environments. By comparing chromosomal positions of ten stably expressed additive QTLs with those previously identified, they might be true QTLs for seed vigor; the regions of QTLs for seed vigor are likely to coincide with QTLs for seed dormancy, seed reserve mobilization, low-temperature germinability, and seedling growth. Using four selected RILs, three cross-combinations were predicted to improve seed vigor; 9 to 10 elite alleles could be pyramided by each combination. The selected RILs and the identified QTLs might be applicable for the improvement of seed vigor by marker-assisted selection (MAS) in rice. Keywords Rice Seed vigor Seed maturity Quantitative trait loci Elite allele