紫花苜蓿QTL与全基因组选择研究进展及其应用

doi:10.11686/cyxb20140636

摘要/Abstract

摘要： 四倍体紫花苜蓿是重要的豆科牧草之一,由于其复杂的遗传背景与二倍体作物相比遗传作图与重要性状数量性状位点(quantitative trait locus,QTL)定位研究相对滞后。然而,二倍体苜蓿的相关研究起步较早,已经建立了高密度遗传图谱和物理图谱,这些研究为四倍体苜蓿遗传作图与QTL定位奠定了基础。随着第三代分子标记与测序技术的快速发展,极大地促进了四倍体苜蓿的高密度遗传图谱构建与QTL定位研究,并借助分子标记辅助育种技术对提高苜蓿选育效率,加速育种进程具有重要意义。本文对苜蓿遗传图谱构建与QTL定位研究及发展趋势进行了总结,并对苜蓿关联作图与全基因组选择的研究进展及应用前景加以概述,旨在为读者就相关研究领域有较全面的了解。

Abstract: Although tetraploid alfalfa is one of the most practically important forage legumes, its genetic mapping and the QTL identification of its significant traits are lagging behind other diploid crops due to its complex genetic background. High-density genetic and physical mapping of diploid alfalfa was initiated several years ago and these studies have laid the theoretical foundation for the genetic mapping and QTL identification of tetraploid alfalfa. This new work on tetraploid alfalfa will be greatly accelerated by the rapid development of third generation molecular markers and sequencing technology. On this basis it will be possible to increase the efficiency of alfalfa breeding programs, especially by using marker-assisted selection. This paper reviews the genetic map construction and QTL analysis of alfalfa. It outlines research progress and the prospects of association mapping and genomic selection in the future.

中图分类号:

S816

康俊梅,张铁军,王梦颖,张怡,杨青川. 紫花苜蓿QTL与全基因组选择研究进展及其应用[J]. 草业学报, 2014, 23(6): 304-312.

KANG Jun-mei,ZHANG Tie-jun,WANG Meng-ying,ZHANG Yi,YANG Qing-chuan. Research progress in the quantitative trait loci (QTL) and genomic selection of alfalfa[J]. Acta Prataculturae Sinica, 2014, 23(6): 304-312.

参考文献

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参考文献：
[1]Sumberg J E, Murphy R P, Lowe C C. Selection for fiber and protein concent ration in a diverse alfalfa population[J]. Crop Science, 1983, 23: 11214.
[2]Michaud R, Lehman W F, Rumbaugh M D. World distribution and historical development[A]. In: Hanson, Barnes D K, Hill Jr. Alfalfa and Alfalfa Improvement, Agronomy Monograph No. 29[M]. Madison American Society of Agronomy, 1988: 25291.
[3]Brummer E C, Kochert G, Bouton J H. RFLP variation in diploid and tetraploid alfalfa[J].Theoretical and Applied Genetics, 1991, 83: 89-96.
[4]Brummer E C, Bouton J H, Kochert G. Development of an RFLP map in diploid alfalfa[J]. Theoretical and Applied Genetics, 1993, 86: 329-332.
[5]Botstein D, White R L, Skolnick M. Construction of a genetic linkage map in man using restriction fragment length polymorphisms[J]. American Journal of Human Genetics, 1990, 32(3): 314-331.
[6]Diwan N, Bouton J H, Kochert G. Mapping of simple sequence repeat (SSR) DNA markers in diploid and tetraploid alfalfa[J]. Theoretical and Applied Genetics, 2000, 101: 165-172.
[7]姜健, 杨宝灵, 夏彤, 等. 紫花苜蓿耐盐种质资源的遗传多样性分析[J]. 草业学报, 2011, 20(5): 119-125.
[8]Kiss B G, Csandadi G, Kalmam K. Construction of basic genetic map for alfalfa using RFLP, RAPD, isozyme and morphological markers[J]. Molecular & General Genetics, 1993, 238: 129-137.
[9]Echt C S, Kidwell K K, Knapp S J. Linkage mapping in diploid alfalfa (Medicago sativa L.)[J]. Genome, 1994, 37: 61-71.
[10]Mengoni A, Gori A, Bazzigalupo M. Use of RAPD and microsatellite (SSR) to assess genetic relationships among populations of tetraploid alfalfa, Medicago sativa[J]. Plant Breeding, 2000, 193: 311-317.
[11]刘曙娜, 于林清, 周延林, 等. 利用RAPD技术构建四倍体苜蓿遗传连锁图谱[J]. 草业学报, 2012, 21(1): 170-175.
[12]Kalp Endre L, Zimnyi G. Construction of an improved linkage map of diploid alfalfa (Medicago sativa)[J]. Theoretical and Applied Genetics, 2000, 100: 641-657.
[13]Yu K F, Pauls K P. Rapid estimation of genetic relatedness among heterogeneous populations of alfalfa by random amplification of bulked genomic DNA samples[J]. Theoretical and Applied Genetics, 1993, 86: 788-794.
[14]Brouwer D J, Osborn T C. A molecular marker linkage map of tetraploid alfalfa (Medicago sativa L.)[J]. Theoretical and Applied Genetics, 1999, 99: 1194-1200.
[15]Sledge M K, Ray I M, Jiang G. An expressed sequence tag SSR map of tetraploid alfalfa (Medicago sativa L.)[J]. Theoretical and Applied Genetics, 2005, 111: 980-992.
[16]Hackett C A, Pande B, Bryan G J. Constructing linkage maps in autotetraploid species using simulated annealing[J]. Theoretical and Applied Genetics, 2003, 106: 1107-1115.
[17]Julier B, Flajoulot S, Barre P. Construction of two genetic linkage maps in cultivated tetraploid alfalfa (Medicago sativa) using microsatellite and AFLP markers[J]. BMC Plant Biology, 2003, 3: 1-19.
[18]Han Y, Kang Y, Torres-Jerez I. Genome-wide SNP discovery in tetraploid alfalfa using 454 sequencing and high resolution melting analysis[J]. BMC Genomics, 2011, 12: 350.
[19]Han Y, Khu D M, Monteros M J. High-resolution melting analysis for SNP genotyping and mapping in tetraploid alfalfa (Medicago sativa L.)[J]. Molecular Breeding, 2012, 29: 489-501.
[20]Han Y, Ray I M, Sledge M K. Drought tolerance in tetraploid alfalfa[A]. Multifunctional grasslands in a changing world, Volume II: XXI International Grassland Congress and VIII International Rangeland Congress[C]. Hohhot, China, 2008: 419.
[21]Khu D M, Reyno R, Han Y. Identification of aluminum tolerance QTLs in tetraploid alfalfa[J]. Crop Science, 2012, 53: 148-163.
[22]Gou J, Han Y, Li X. SNP identification in genes associated with lignin content and forage composition in alfalfa[C]. Plant & Animal Genomes XVII Conference, 2011: 10-14.
[23]Li X, Wei Y, Moore K J. Association mapping of biomass yield and stem composition in a tetraploid alfalfa breeding population[J]. Plant Genome, 2011, 4: 24-35.
[24]Zhang Y, Sledge M K, Bouton J H. Genome mapping of white clover (Trifolium repens L.) and comparative analysis within the Trifolieae using cross-species SSR markers[J].Theoretical and Applied Genetics, 2007, 114: 1367-1378.
[25]Sakiroglu M, Doyle J J, Brummer E C. Inferring population structure and genetic diversity of broad range of wild diploid alfalfa (Medicago sativa L.) accessions using SSR markers[J]. Theoretical and Applied Genetics, 2010, 121: 403-415.
[26]Robins J G, Luth D, Campbell I A. Genetic mapping of biomass production in tetraploid alfalfa[J]. Crop Science, 2007, 47: 1-10.
[27]Li X, Wang X, Brummer E C. Prevalence of segregation distortion in diploid alfalfa and its implications for genetics and breeding applications[J]. Theoretical and Applied Genetics, 2011, 123: 667-679.
[28]Narasimhamoorthy B, Bouton J H, Olsen K M. Quantitative trait loci and candidate gene mapping of aluminum tolerance in diploid alfalfa[J]. Theoretical and Applied Genetics, 2007, 114: 901-913.
[29]Pupilli F, Businelli S, Paolocci F. Extent of RFLP variability in tetraploid populations of alfalfa (Medicago sativa)[J]. Plant Breeding, 1996, 115: 106-112.
[30]Li X H, Brummer E C. Inbreeding depression for fertility and biomass in advanced generations of inter- and intra-subspecific hybrids of tetraploid alfalfa[J]. Crop Science, 2009, 49: 13-19.
[31]Robins J G, Bauchan G R, Brummer E C. Genetic mapping forage yield, plant height, and regrowth at multiple harvests in tetraploid alfalfa (Medicago sativa L.)[J]. Crop Science, 2007, 47: 11-18.
[32]Brouwer D J, Duke S H, Osborn T C. Mapping genetic factors associated with winter hardiness, fail growth, and freezing injury in autotetraploid alfalfa[J]. Crop Science, 2000, 40: 1387-1396.
[33]Alarcon Zuniga B, Scott P, Brummer E C. Quantitative trait locus mapping of winter hardiness metabolites in autotetraploid alfalfa (M. sativa)[A]. In: Hopkins A. Molecular Breeding of Forage and Turf[M]. Kluwer: Dordrecht, the Netherlands, 2004: 97-104.
[34]Robins J G, Hansen J L, Viands D R. Genetic mapping of persistence in tetraploid alfalfa[J]. Crop Science, 2008, 48: 1780-1786.
[35]姜格格, 宋丽莉, 郭东林, 等. 蒺藜苜蓿耐酸铝性状的全基因组关联分析[J]. 草业学报, 2013, 22(4): 170-178.
[36]Julier B, Bernard K, Gibelin C. QTL for water use efficiency in alfalfa[A]. In: Huyghe C. Sustainable Use of Genetic Diversity in Forage and Turf Breeding[M]. Berlin, Germany: Springer, 2010: 433-436.
[37]Beavis W D. QTL analyses: power, precision, and accuracy[A]. In: Paterson A. Molecular Dissection of Complex Traits[M].New York, NY, USA: CGC Press, 1998: 145-162.
[38]Xu S. Theoretical basis of the Beavis effect[J]. Genetics, 2003, 165: 2259-2268.
[39]Li X, Acharya A, Farmer A D,et al. Prevalence of single nucleotide polymorphism among 27 diverse alfalfa genotypes as assessed by transcriptome sequencing[J]. BMC Genomics, 2012, 13: 568.
[40]Musial J M, Mackie J M, Armour D J. Identification of QTL for resistance and susceptibility to Stagonospora meliloti in autotetraploid lucerne[J]. Theoretical and Applied Genetics, 2007, 114: 1427-1435.
[41]Endre G, Kalo P, Kevei Z. Genetic mapping of the non-nodulation phenotype of the mutant MN-1008 in tetraploid alfalfa (Medicago sativa)[J]. Molecular Genetics and Genomics, 2002, 266: 1012-1019.
[42]Endre G, Kereszt A, Kevei Z. A receptor kinase gene regulating symbiotic nodule development[J]. Nature, 2002, 417: 962-966.
[43]Yang S, Gao M, Xu C. Alfalfa benefits from Medicago truncatula: the RCT1 gene from M. truncatula confers broad-spectrum resistance to anthracnose in alfalfa[J]. Proceedings of the National Academy of Sciences, USA, 2008, 105: 12164-12169.
[44]Kamphuis L, Lichtenzveig J, Oliver R. Two alternative recessive quantitative trait loci influence resistance to spring black stem and leaf spot in Medicago truncatula[J]. BMC Plant Biology, 2008, 8(30): 1-12.
[45]Moreau D, Burstin J, Aubert G. Using a physiological framework for improving the detection of quantitative trait loci related to nitrogen nutrition in Medicago truncatula[J]. Theoretical and Applied Genetics, 2012, 124: 755-768.
[46]Young N D, Debellé F, Oldroyd G E D. The Medicago genome provides insight into the evolution of rhizobial symbioses[J]. Nature, 2011, 480: 520-524.
[47]Pierre J B, Huguet T, Barre P. Detection of QTLs for flowering date in three mapping populations of the model legume species Medicago truncatula[J]. Theoretical and Applied Genetics, 2008, 117: 609-620.
[48]Julier B, Huguet T, Chardon F. Identification of quantitative trait loci influencing aerial morphogenesis in the model legume Medicago truncatula[J]. Theoretical and Applied Genetics, 2007, 114: 1391-1406.
[49]Choi H K, Kim D, Uhm T. A sequence-based genetic map of Medicago truncatula and comparison of marker colinearity with M. sativa[J]. Genetics, 2004, 166: 1463-1502.
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