[1] Ganal M W, Altmann T, R?觟der M S. SNP identification in crop plants[J]. Current Opinion in Plant Biology, 2009, 12(2): 211-217.
[2] Kaur S, Francki M G, Forster J W. Identification, characterization and interpretation of single-nucleotide sequence variation in allopolyploid crop species[J]. Plant Biotechnology Journal, 2012, 10(2): 125-138.
[3] Senchina D S, Alvarez I, Cronn R C, et al. Rate variation among nuclear genes and the age of polyploidy in Gossypium[J]. Molecular Biology and Evolution, 2003, 20(4): 633 -643.
[4] Lee G A, Koh H J, Chung H K, et al. Development of SNP-based CAPS and dCAPS markers in eight different genes involved in starch biosynthesis in rice[J]. Molecular Breeding, 2009, 24(1): 93-101.
[5] Ewing B, Green P. Base-calling of automated sequencer traces using phred. Ⅱ. Error probabilities[J]. Genome Research, 1998, 8: 186-194.
[6] Tang Jifeng, Vosman B, Voorrips R E, et al. QualitySNP: a pipeline for detecting single nucleotide polymorphisms and insertions/deletions in EST data from diploid and polyploid species[J/OL]. BMC Bioinformatics, 2006, 7: 438 [2016-10-17]. http://bm- cbioinformatics.biomedcentral.com/articles/10.1186/1471-2105- 7-438. DOI: 10.1186/1471-2105-7-438.
[7] Altschul S F, Madden T L, Schaffera A, et al. Gapped BLAST and PSI-BLAST: A new generation of protein database search program[J]. Nucleic Acids Research, 1997, 25: 3389-3402.
[8] Picoultnewberg L, Ideker T E, Pohl M G, et al. Mining SNPs from EST database[J]. Genome Research, 1999, 9(2): 167-174.
[9] Torjk O, Berger D, Meyer R C, et al. Establishment of a high-efficiency SNP-based framework marker set for Arabidopsis[J].The Plant Journal, 2003, 36(1): 122-140.
[10] Feltus F A, Wan J, Schulze S R, et al. An SNP resource for rice genetics and breeding based on subspecies indica and japonica genome alignments[J]. Genome Research, 2004, 14(9): 1812- 1819.
[11] Batley J, Barker G, O' Sullivan H, et al. Mining for single nucleotide polymorphisms and insertions/deletions in maize expressed sequence tag data[J]. Plant Physiology, 2003, 132(1): 84-91.
[12] Rustgi S, Bandopadhyay R, Balyan H S, et al. EST-SNPs in bread wheat: discovery, validation, genotyping and haplotype structure[J]. Czech Journal of Genetics and Plant Breeding, 2009, 45: 106-116.
[13] Kota R, Varshney R K, Prasad M, et al. EST-derived single nucleotide polymorphism markers for assembling genetic and physical maps of the barley genome[J]. Functional & Integrative Genomics, 2008, 8(3): 223-233.
[14] Yamamoto N, Tsugane T, Watanabe M, et al. Expressed sequence tags from the laboratory-grown miniature tomato (Lycopersicon esculentum) cultivar Micro-Tom and mining for single nucleotide polymorphisms and insertions/deletions in tomato cultivars[J]. Gene, 2005, 356: 127-134.
[15] Dantec L L, Chagné D, Pot D, et al. Automated SNP detection in expressed sequence tags: Statistical considerations and application to maritime pine sequences[J]. Plant Molecular Biology, 2004, 54(3):461-470.
[16] Chagné D, Gasic K, Crowhurst R N, et al. Development of a set of SNP markers present in expressed genes of the apple[J/OL]. Genomics, 2008, 92(5): 353 [2016-10-17]. http://www.sciencedirect.com/science/article/pii/S0888754308001808. DOI: 10. 1016/ j.ygeno.2008.07.008.
[17] Van Deynze A, Stoffel K, Lee M, et al. Sampling nucleotide diversity in cotton[J/OL]. BMC Plant Biology, 2009, 9(1): 125 [2016-10-17]. https://bmcplantbiol.biomedcentral.com/articles/ 10.1186/1471-2229-9-125. DOI: 10.1186/1471-2229-9-125.
[18] Hulse-Kemp A M, Ashrafi H, Stoffel K, et al. BAC-end sequence-based SNP mining in allotetraploid cotton (Gossypium) utilizing resequencing data, phylogenetic inferences, and perspectives for genetic mapping[J]. Genes Genomes Genetics, 2015, 5(6): 1095-1105.
[19] Zhu Qianhao, Spriggs A, Taylor J M, et al. Transcriptome and complexity-reduced, DNA-based identification of intraspecies single-nucleotide polymorphisms in the polyploid Gossypium hirsutum L.[J]. Genes Genomes Genetics, 2014, 4(10): 1893- 1905.
[20] Li Ximei, Gao Wenhui, Guo Huanle, et al. Development of EST-based SNP and InDel markers and their utilization in tetraploid cotton genetic mapping[J/OL]. BMC Genomics, 2014, 15(1): 1046 [2016-10-17]. http://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-15-1046. DOI: 10.1186/1471- 2164-15-1046.
[21] Wang Sen, Chen Jiedan, Zhang Wenpan, et al. Sequence-based ultra-dense genetic and physical maps reveal structural variations of allopolyploid cotton genomes[J/OL]. Genome Biology, 2015, 16 (1): 108 [2016-10-17]. http://genomebiology.biomedcentral.com/articles/10.1186/s13059-015-0678-1. DOI: 10.1186/ s13059-015-0678-1. |