作为群体遗传学一种新的表现形式,群体基因组学是将基因组概念和技术与群体遗传学理论体系相结合,通过覆盖全基因组范围内的多态位点的分布式样推测位点特异性效应和全基因组效应,从而提升人们对微进化的理解。近年来,随着第二代高通量测序技术的出现和改进,完成基因组测序的植物种类迅速增加,大规模的重测序也随之开展。与此同时,在一些尚未完成基因组测序的植物物种中,也开展了一些平行测序。这些重测序和平行测序极大地促进了群体基因组学的发展,加深了人们对相关植物种群在基因组水平上的遗传多样性、连锁不平衡水平、选择作用、群体历史及复杂性状的分子机理等群体基因组学方面的认识。本文简要介绍了群体基因组学的概念、研究方法等,重点综述了基于高通量测序的植物群体基因组学的研究动态,展望了植物群体基因组学的发展前景并讨论了存在的问题,以期为相关研究提供借鉴和参考。
[1] Gulcher J, Stefansson K. Population genomics: Laying the groundwork for genetic disease modelling and targeting. Clin Chem Lab Med , 1998, 36(8): 523-527.
[2] Goldstein DB, Weale ME. Population genomics: Linkage disequilibrium holds the key. Curr Biol , 2001, 11(14): R576-R579.
[3] Jorde LB, Watkins WS, Bamshad MJ. Population genomics: A bridge from evolutionary history to genetic medicine. Hum Mol Genet , 2001, 10(20): 2199-2207.
[4] Gibson G, Mackay TF. C. Enabling population and quantitative genomics. Genet Res , 2002, 80(1): 1-6.
[5] Black WC, Baer CF, Antolin MF, DuTeau NM. Population genomics: Genome-wide sampling of insect populations. Annu Rev Entomol , 2001, 46(1): 441-469.
[6] Luikart G, England PR, Tallmon D, Jordan S, Taberlet P. The power and promise of population genomics: From genotyping to genome typing. Nat Rev Genet , 2003, 4(12): 981-994.
[7] Ellegren H. Genome sequencing and population genomics in non-model organisms. Trends Ecol Evol , 2014, 29(1): 51-63.
[8] Mardis ER. The impact of next-generation sequencing technology on genetics. Trends Genet , 2007, 24(3): 133-141.
[9] Craig DW, Pearson JV, Szelinger S, Sekar A, Redman M, Corneveaux JJ, Pawlowski TL, Laub T, Nunn G, Stephan DA, Homer N, Huentelman MJ. Identification of genetic variants using bar-coded multiplexed sequencing. Nat Methods , 2008, 5(10): 887-893.
[10] Cronn R, Liston A, Parks M, Gernandt DS, Shen RK, Mockler T. Multiplex sequencing of plant chloroplast genomes using solexa sequencing-by-synthesis technology. Nucleic Acids Res , 2008, 36(19): e122.
[11] Stratton M. Genome resequencing and genetic variation. Nat Biotechnol , 2008, 26(1): 65-66.
[12] Xu XY, Bai GH. Whole-genome resequencing: Changing the paradigms of SNP detection, molecular mapping and gene discovery. Mol Breeding , 2015, 35: 33.
[13] Begun DJ, Holloway AK, Stevens K, Hillier LW, Poh YP, Hahn MW, Nista PM, Jones CD, Kern AD, Dewey CN, Pachter L, Myers E, Langley CH. Population genomics: Whole-genome analysis of polymorphism and divergence in Drosophila simulans. PLoS Biol , 2007, 5(11): e310.
[14] Yu P, Wang CH, Xu Q, Feng Y, Yuan XP, Yu HY, Wang YP, Tang SX, Wei XH. Detection of copy number variations in rice using array-based comparative genomic hybridization. BMC Genomics , 2011, 12: 372.
[15] McHale LK, Haun WJ, Xu WW, Bhaskar PB, Anderson JE, Hyten DL, Gerhardt DJ, Jeddeloh JA, Stupar RM. Structural variants in the soybean genome localize to clusters of biotic stress-response genes. Plant Physiol , 2012, 159(4): 1295-1308.
[16] Pasam RK, Sharma R, Malosetti M, van Eeuwijk FA, Haseneyer G, Kilian B, Graner A. Genome-wide association studies for agronomical traits in a world wide spring barley collection. BMC Plant Biol , 2012, 12: 16.
[17] Nimmakayala P, Levi A, Abburi L, Abburi VL, Tomason YR, Saminathan T, Vajja VG, Malkaram S, Reddy R, Wehner TC, Mitchell SE, Reddy UK. Single nucleotide polymorphisms generated by genotyping by sequencing to characterize genome-wide diversity, linkage disequilibrium, and selective sweeps in cultivated watermelon. BMC Genomics , 2014, 15: 767.
[18] Wen ZX, Boyse JF, Song QJ, Cregan PB, Wang DC. Genomic consequences of selection and genome-wide association mapping in soybean. BMC Genomics , 2015, 16: 671.
[19] Wu J, Lenchik NI, Gerling IC. Approaches to reduce false positives and false negatives in the analysis of microarray data: applications in type 1 diabetes research. BMC Genomics , 2008, 9(Suppl. 2): S12.
[20] Davey JW, Hohenlohe PA, Etter PD, Boone JQ, Catchen JM, Blaxter ML. Genome-wide genetic marker discovery and genotyping using next-generation sequencing. Nat Rev Genet , 2011, 12(7): 499-510.
[21] Huang XH, Feng Q, Qian Q, Zhao Q, Wang L, Wang AH, Guan JP, Fan DL, Weng QJ, Huang T, Dong GJ, Sang T, Han B. High-throughput genotyping by whole-genome resequencing. Genome Res , 2009, 19(6): 1068-1076.
[22] Imelfort M, Edwards D. De novo seque
