Abstract
Embryo sac sterility is one of the main reasons for infertility of indica–japonica hybrids and S5 is a major locus for embryo sac fertility. The present study was planned: (1) to sequence germplasm not carrying \({S_{\it{5}}}^{\it{n}}\) gene to ascertain their sequence diversity and domestication of Asian cultivated rice (indica–japonica), (2) to identify genotypes of ORF3 and ORF4 gene in materials with S5 gene coding region variation, and (3) to evaluate the effect of S5 gene coding region variation on embryo sac sterility. A total of 273 materials were sequenced, including 134 cultivars of Oryza sativa and 139 accessions of Oryza rufipogon. The results showed that 273 materials had different degrees of variation in S5 gene sequence compared with control cultivars. Coding region variation mainly occurred in exon 1 and exon 2, including 3 variable sites, of which 8 materials had 9 bp deletion at 177–185 bp, 1 materials had 12 bp deletion at 1,479–1,490 bp. Phylogenetic analysis suggested independent origin of indica and japonica subspecies from wild rice. Further, we found that all materials carrying S5 gene coding region variation were ORF3+, ORF4+, and ORF5+. Testcross hybrids were developed by crossing typical indica and japonica cultivars with lines carrying large differences in S5 coding region. Substantial evidence showed that ORF3+ is a major type for overcoming hybrid sterility, and S5 gene coding region variation had insignificant effect on embryo sac fertility. Genetic nucleotide diversity of \({S_{\it{5}}}^{\it{i}}\) and \({S_{\it{5}}}^{\it{j}}\) indicated that S5 is a very conservative gene. Further, it suggested that indica and japonica subspecies originated separately from ancestral wild rice.
Similar content being viewed by others
References
Chang TT (1976) Origin, evolution, cultivation, dissemination, and diversification of Asian and African rice. Euphytica 25:425–441
Chen JJ, Ding JH, Ouyang YD, Du HY, Yang YJ, Cheng K, Zhao J, Qiu SQ, Zhang XL, Yao JL, Liu KD, Wang L, Xu CG, Li XH, Xue YB, Xia M, Ji Q, Zhang QF (2008) A triallelic system of S5 is a major regulator. Proc Natl Acad Sci USA 105:11436–11441
Cheng CY, Motohashi R, Ohtsubo E (2003) Polyphyletic origin of cultivated rice: based on the interspersion pattern of SINEs. Mol Biol Evol 20:67–75
Dai XJ, Yang YZ, Zhou L, Ou LJ, Liang MZ, Li WJ, Kang GP, Chen LB (2012) Analysis of indica- and japonica-specific markers of Oryza sativa and their applications. Plant Syst Evol 298:287–296
Du H, Ouyang Y, Zhang C, Zhang QF (2011) Complex evolution of S5, a major reproductive barrier regulator, in the cultivated rice Oryza sativa and its wild relatives. New Phytol 191:275–287
Fu YX (1997) Statistical tests of neutrality of mutations against population growth, hitchhiking and background selection. Genetics 147:915–925
Gao LZ, Innan H (2008) Nonindependent domestication of the two rice subspecies, Oryza sativa ssp. indica and ssp. japonica, demonstrated by multilocus microsatellites. Genetics 179:965–976
Garris AJ, Tai TH, Coburn J, Kresovich S, McCouch S (2005) Genetic structure and diversity in Oryza sativa L. Genetics 169:1631–1638
Hu CY, Zeng YX, Lu XD, Li JQ (2009) High embryo-sac fertility and diversity of abnormal embryo-sacs detected in autotetraploid indica/japonica hybrids in rice by whole-mount eosin B-staining microscopy. Plant Breed 128:187–192
Ikehashi H (1984) Variety screening of compatibility types revealed in F1 fertility of distant crosses in rice. Jpn J Breed 34:304–313
Ikehashi H, Araki H (1986) Genetics of F1 sterility in remote crosses of rice. Rice Genetics. IRRI, Manila, pp 119–130
Kumar S, Nei M, Dudley J, Tamura K (2008) MEGA: a biologist-centric software for evolutionary analysis of DNA and protein sequences. Brief Bioinform 9:299–306
Li HB, Li CG, Chen ZM (1995) The study on indica–japonica hybrids’ stability. Jiangsu J Agri Sci 11:7–11
Li C, Zhou A, Sang T (2006) Rice domestication by reducing shattering. Science 311:1936–1939
Liu KD, Wang J, Li HB, Xu GC, Liu AM, Li XH, Zhang QF (1997) A genome-wide analysis of wide compatibility in rice and the precise location of the S5 locus in the molecular map. Theor Appl Genet 95:809–814
Liu B, Li JQ, Liu XD, Shahid MQ, Shi LG, Lu YG (2011) Identification of neutral genes at pollen sterility loci Sd and Se of cultivated rice (Oryza sativa) with wild rice (O. rufipogon) origin. Genet Mol Res 10:3435–3445
Londo JP, Chiang YC, Hung KH, Chiang TY, Schaal BA (2006) Phylogeography of Asian wild rice, Oryza rufipogon, reveals multiple independent domestications of cultivated rice, Oryza sativa. Proc Natl Acad Sci USA 103:9578–9583
Long YM, Zhao LF, Niu BX, Su J, Wu H, Chen YL, Zhang QY, Guo JX, Zhuang CX, Mei MT, Xia JX, Liu YG (2008) Hybrid male sterility in rice controlled by interaction between divergent alleles of two adjacent genes. Proc Natl Acad Sci USA 105:18871–18876
Molina J, Sikora M, Garud N, Flowers JM, Rubinstein S, Reynolds A, Huang P, Jackson S, Schaal BA, Michael D (2011) Molecular evidence for a single evolutionary origin of domesticated rice. Proc Natl Acad Sci USA 108:8351–8356
Nei M (1987) Molecular evolutionary genetics. Columbia University Press, New York
Oka HI (1974) Analysis of genes controlling F1 sterility in rice by the use of isogenic lines. Genetics 77:521–534
Oka HI (1988) Origin of cultivated rice. Elsevier, Amsterdam
Purugganan MD, Fuller DQ (2009) The nature of selection during plant domestication. Nature 457:843–848
Qiu SQ, Liu K, Jiang X, Song CG, Xu XH, Zhang QF (2005) Delimitation of the rice wide compatibility gene S n 5 to a 40-kb DNA fragment. Theor Appl Genet 111:1080–1086
Rozas J, Sánchez-Delbarrio JC, Messeguer X, Rozas J (2003) DNA polymorphism analysis by the coalescent and other methods. Bioinformatics 19:2496–2497
Shahid MQ, Sun JF, Wei CM, Zhang P, Liu XD (2010) Studies on the abnormality of embryo sac and pollen fertility in autotetraploid rice during different growing seasons. Pak J Bot 42:7–19
Shahid MQ, Chen FY, Li HY, Wang SZ, Chen PF, Lin SQ, Liu XD, Lu YG (2013) Double-Neutral genes, Sa-n and Sb-n, for pollen fertility in rice to overcome indica × japonica hybrid sterility. Crop Sci 53:164–176
Song X, Qi QS, Xu CG (2005) Genetic dissection of embryo-sac fertility, pollen fertility, and their contributions to spikelet fertility of intersubspecific hybrids in rice. Theor Appl Genet 110:205–211
Sundaram RM, Sakthivel K, Hariprasad AS, Ramesha MS, Viraktamath BC, Neeraja CN, Balachandran SM, Rani N, Sandhya P, Hari Y (2010) Development and validation of a PCR-based functional marker system for the major wide-compatible gene locus S5 in rice. Mol Breed 26:719–727
Tajima F (1989) Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123:585–595
Tan L, Li X, Liu F, Sun X, Li C, Fu Y, Cai H (2008) Control of a key transition from prostrate to erect growth in rice domestication. Nat Genet 40:1360–1364
Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG (1997) The Clustal-X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 24:4876–4882
Tong JF, Li YH, Yang YX, Chen ZX, Wang L, Li JQ, Shahid MQ, Liu XD, Lu YG (2011) Molecular evolution of rice S n 5 and functional comparison among different sequences. Chin Sci Bull 56:2016–2024
Wan J, Ikehashi H (1995) Identification of a new locus S-16 causing hybrid sterility in native rice varieties (Oryza sativa L.) from Tai-hu lake region and Yunnan Province, China. Breed Sci 45:461–470
Wan J, Yanagihara S, Kato H (1993) Multiple alleles at a new locus causing hybrid sterility between a Korean indica variety and a japonica variety in rice (Oryza sativa L.). Jpn J Breed 43:507–516
Wan J, Yamaguchi Y, Kato H, Ikehashi H (1996) Two new loci for hybrid sterility in cultivated rice (Oryza sativa L.). Theor Appl Genet 92:183–190
Watterson GA (1975) On the number of segregating sites in genetical models without recombination. Theor Popul Biol 7:256–276
Wei CM, Wan L, Yang YX, Chen ZX, Shahid MQ, Li JQ, Liu XD, Lu YG (2010) Identification of an S n 5 allele in Oryza rufipogon Griff and its effect on embryo sac fertility. Chin Sci Bull 55:1255–1262
Xu CG (1995) Pollen attached on the stigma and germination observation in subspecies and intersubspecies. Huazhong Agri Uni 14:421–425
Yanagihara S, Kato H, Ikehashi H (1995) A new locus for multiple alleles causing hybrid sterility between an Aus variety and javanica varieties in rice (Oryza sativa L.). Theor Appl Genet 90:182–188
Yang YX, Wu JW, Chen ZX, Wang L, Guo HB, Li JQ, Liu XD, Lu YG (2009) Mining rice new germplasm containing S n 5 gene by functional molecular marker and sequencing. Chin Sci Bull 54:3258–3264
Yang JY, Zhao XB, Cheng K, Du HY, Ouyang YD, Chen JJ, Qiu SQ, Huang JH, Jiang YH, Jiang LW, Ding JH, Wang J, Xu CG, Li XH, Zhang QF (2012) A killer-protector system regulates both hybrid sterility and segregation distortion in rice. Science 337:1336–1339
Yu JW (1991) The study on bagging impacted rice seed and seed development. Hybrid Rice 6:40–42
Zhang GQ, Lu YG (1993) The genetic research II on cultivated rice sterility: the gene patterns of pollen sterility. Genetics 20:222–228
Zhang GQ, Lu YG, Liu GG, Yang JC, Zhang H (1994) The genetic research IV on cultivated rice hybrid sterility: genotype of hybrid F1 sterility. Genetics 21:35–42
Zheng KL, Huang N, Bennett J, Khush GS (1995) PCR-based phylogenetic analysis of wide compatibility varieties in Oryza sativa L. Theor Appl Genet 88:65–69
Zhu QH, Ge S (2005) Phylogenetic relationships among A-genome species of the genus Oryza revealed by intron sequences of four nuclear genes. New Phytol 67:249–265
Zhu YG, Yu JH, Yang DC (1996) The breeding on subspecies hybrid F1 genetic affinity and wide compatibility lines. Hubei Agric Sci 28:28–32
Zhuang CX, Zhang GQ, Mei MT, Lu YG (1999) The molecular mapping on pollen sterility loci Sa in cultivated rice F1. Genetics 26:213–218
Acknowledgments
The authors appreciated the supports from Prof. HAN Longzhi for donating the China National Micro-core Rice Collection. We also thank Dr. CHEN Zhixiong, Dr. WANG Lan, Dr. FU Xuelin, Dr. LI Jinquan, Ms. ZHAO Xingjuan, and YU ShuHong for technical assistance. This work was supported by the NSFC (30971756), Guangdong Science and Technology special funds for State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources (2012). The Special Fund for Agro-Scientific Research in the Public Interest (No. 201003021) and the Guangdong Provincial Key Science Foundation.
Author information
Authors and Affiliations
Corresponding authors
Additional information
H. Peng, M. Q. Shahid, Y.-H. Li contributed equally to this work.
Electronic supplementary material
Below is the link to the electronic supplementary material.
Rights and permissions
About this article
Cite this article
Peng, H., Shahid, M.Q., Li, YH. et al. Molecular evolution of S5 locus and large differences in its coding region revealed insignificant effect on indica × japonica embryo sac fertility. Plant Syst Evol 301, 639–655 (2015). https://doi.org/10.1007/s00606-014-1102-0
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s00606-014-1102-0