Genome-wide single nucleotide polymorphisms and insertion–deletions of Oryza sativa L. subsp. japonica cultivars grown near the northern limit of rice cultivation
Single nucleotide polymorphisms (SNPs) and insertions–deletions (InDels) are valuable molecular markers for molecular breeding among genetically closely related cultivars. Rice (Oryza sativa L. subsp. japonica) cultivars grown in Hokkaido (45–42°N), the northernmost region of rice paddy cultivation in Japan, have been bred for over 100 years for adaptation to low summer temperatures together with high yield and good eating quality. In this study, for 10 closely related rice cultivars released in Hokkaido and cultivar Koshihikari, we identified genome-wide SNPs and InDels by next-generation sequencing. More than 29 million reads from the Hokkaido cultivars, each 101 nucleotides long, were uniquely mapped to the Nipponbare reference genome. The average of the total nucleotide length of all uniquely mapped reads corresponded to 10.9 times (3,978 Mb with genome coverage of 90.7 %) the Nipponbare reference genome. An average of 99,955 putative SNPs (1.8 times the number in Koshihikari) and 14,617 putative InDels (also 1.8 times the number in Koshihikari) were detected in Hokkaido cultivars relative to the Nipponbare genome, which enabled analyses of the inheritance of pedigree haplotypes of four cultivars, SNPs and InDels among closely related Hokkaido cultivars, and haplotype blocks unique to Hokkaido cultivars. The comprehensive SNP and InDel data provide DNA marker resources and will facilitate quantitative trait locus analysis of biparental mapping of very closely related Hokkaido cultivars. Furthermore, the haplotype blocks unique to Hokkaido cultivars represent ideal genetic regions for improvement of cultivars to be grown near the northern and southern limits of rice cultivation.
KeywordsSingle nucleotide polymorphism Insertion Deletion Next-generation sequencing Oryza sativa L.
This study was supported in part by the Suhara Memorial Foundation, the Tojuro Iijima Foundation for Food Science and Technology, and Adaptable and Seamless Technology Transfer Program through Target-driven R&D (A-STEP), Japan Science and Technology Agency (JST). Seeds of Hokkaido cultivars were provided by the Central Agricultural Experiment Station, Local Independent Administrative Agency Hokkaido Research Organization, and seeds of Koshihikari were provided by the National Institute of Agrobiological Sciences Genebank. We thank Noboru Shinbashi, Harumi Kikuchi, Toshio Yamamoto, Satoshi Natsume, Hiroki Takagi, Ryohei Terauchi, Kei Sonoyama, Toshihiko Maekawa, Yuuji Hirayama, Hitoshi Kiuchi, Tsutomu Nishimura, and Hirokazu Sato for their valuable suggestions throughout the study.
- DePristo MA, Banks E, Poplin R, Garimella KV, Maguire JR, Hartl C, Philippakis AA, del Angel G, Rivas MA, Hanna M, McKenna A, Fennell TJ, Kernytsky AM, Sivachenko AY, Cibulskis K, Gabriel SB, Altshuler D, Daly MJ (2011) A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat Genet 43:491–498PubMedCrossRefPubMedCentralGoogle Scholar
- Hillier LW, Marth GT, Quinlan AR, Dooling D, Fewell G, Barnett D, Fox P, Glasscock JI, Hickenbotham M, Huang W, Magrini VJ, Richt RJ, Sander SN, Stewart DA, Stromberg M, Tsung EF, Wylie T, Schedl T, Wilson RK, Mardis ER (2008) Whole-genome sequencing and variant discovery in C. elegans. Nat Methods 5:183–188PubMedCrossRefGoogle Scholar
- Hori K, Sugimoto K, Nonoue Y, Ono N, Matsubara K, Yamanouchi U, Abe A, Takeuchi Y, Yano M (2010) Detection of quantitative trait loci controlling pre-harvest sprouting resistance by using backcrossed populations of japonica rice cultivars. Theor Appl Genet 120:1547–1557PubMedCrossRefPubMedCentralGoogle Scholar
- Hyten DL, Cannon SB, Song Q, Weeks N, Fickus EW, Shoemaker RC, Specht JE, Farmer AD, May GD, Cregan PB (2010a) High-throughput SNP discovery through deep resequencing of a reduced representation library to anchor and orient scaffolds in the soybean whole genome sequence. BMC Genom 11:38CrossRefGoogle Scholar
- Kumar S, Banks TW, Cloutier S (2012) SNP discovery through next-generation sequencing and its applications. Int J Plant Genomics 2012:Article ID 831460Google Scholar
- Lai J, Li R, Xu X, Jin W, Xu M, Zhao H, Xiang Z, Song W, Ying K, Zhang M, Jiao Y, Ni P, Zhang J, Li D, Guo X, Ye K, Jian M, Wang B, Zheng H, Liang H, Zhang X, Wang S, Chen S, Li J, Fu Y, Springer NM, Yang H, Wang J, Dai J, Schnable PS, Wang J (2010) Genome-wide patterns of genetic variation among elite maize inbred lines. Nat Genet 42:1027–1030PubMedCrossRefGoogle Scholar
- Matsubara K, Kono I, Hori K, Nonoue Y, Ono N, Shomura A, Mizubayashi T, Yamamoto S, Yamanouchi U, Shirasawa K, Nishio T, Yano M (2008) Novel QTLs for photoperiodic flowering revealed by using reciprocal backcross inbred lines from crosses between japonica rice cultivars. Theor Appl Genet 117:935–945PubMedCrossRefGoogle Scholar
- Okumoto Y, Ichitani K, Inoue H, Tanisaka T (1997) Photoperiod insensitivity gene essential to the varieties grown in the northern limit region of paddy rice (Oryza sativa L.) cultivation. In: Tigerstedt PMA (ed) Adaptation in plant breeding. Kluwer Academic Publisher, Netherlands, pp 77–80CrossRefGoogle Scholar
- Smith DR, Quinlan AR, Peckham HE, Makowsky K, Tao W, Woolf B, Shen L, Donahue WF, Tusneem N, Stromberg MP, Stewart DA, Zhang L, Ranade SS, Warner JB, Lee CC, Coleman BE, Zhang Z, McLaughlin SF, Malek JA, Sorenson JM, Blanchard AP, Chapman J, Hillman D, Chen F, Rokhsar DS, McKernan KJ, Jeffries TW, Marth GT, Richardson PM (2008) Rapid whole-genome mutational profiling using next-generation sequencing technologies. Genome Res 18:1638–1642PubMedCrossRefPubMedCentralGoogle Scholar
- Takeuchi Y, Hori K, Suzuki K, Nonoue Y, Takemoto-Kuno Y, Maeda H, Sato H, Hirabayashi H, Ohta H, Ishii T, Kato H, Nemoto H, Imbe T, Ohtsubo K, Yano M, Ando I (2008) Major QTLs for eating quality of an elite Japanese rice cultivar, Koshihikari, on the short arm of chromosome 3. Breed Sci 58:437–445CrossRefGoogle Scholar
- Wang DG, Fan JB, Siao CJ, Berno A, Young P, Sapolsky R, Ghandour G, Perkins N, Winchester E, Spencer J, Kruglyak L, Stein L, Hsie L, Topaloglou T, Hubbell E, Robinson E, Mittmann M, Morris MS, Shen N, Kilburn D, Rioux J, Nusbaum C, Rozen S, Hudson TJ, Lipshutz R, Chee M, Lander ES (1998) Large-scale identification, mapping, and genotyping of single- nucleotide polymorphisms in the human genome. Science 280:1077–1082PubMedCrossRefGoogle Scholar
- Xu Y, Lu Y, Yan J, Babu R, Hao Z, Gao S, Zhang S, Li J, Vivek B, Magorokosho C (2008) SNP-chip-based genomewide scans for germplasm evaluation, marker-trait association analysis and development of a molecular breeding platform in maize. In: Proceedings of 14th Australiasian plant breeding conference (APBC) and 11th congress of the society for the advancement of breeding research in Asia and Oceania (SABRAO) 10–14 August 2009, Cairns Convention Centre, Cairns, Tropical North Queensland, AustraliaGoogle Scholar
- Zhao K, Wright M, Kimball J, Eizenga G, McClung A, Kovach M, Tyagi W, Ali ML, Tung CW, Reynolds A, Bustamante CD, McCouch SR (2010) Genomic diversity and introgression in O. sativa reveal the impact of domestication and breeding on the rice genome. PLoS ONE 5:e10780PubMedCrossRefPubMedCentralGoogle Scholar
- Zhao K, Tung CW, Eizenga GC, Wright MH, Ali ML, Price AH, Norton GJ, Islam MR, Reynolds A, Mezey J, McClung AM, Bustamante CD, McCouch SR (2011) Genome-wide association mapping reveals a rich genetic architecture of complex traits in Oryza sativa. Nat Commun 2:467PubMedCrossRefPubMedCentralGoogle Scholar