000			03784nab|a22004217a|4500
999			_c63661 _d63653
001			63661
003			MX-TxCIM
005			20240826225837.0
008			200910s2021||||xxk|||p|op||||00||0|eng|d
022			_a1471-2229
024	8		_ahttps://doi.org/10.1186/s12870-021-02932-8
040			_aMX-TxCIM
041			_aeng
100	0		_aZhengjie Chen _919713
245	1	0	_aDevelopment of genic KASP SNP markers from RNA-Seq data for map-based cloning and marker-assisted selection in maize
260			_aLondon (United Kingdom) : _bBioMed Central, _c2021.
500			_aPeer review
500			_aOpen Access
520			_aBackground: Maize is one of the most important field crops in the world. Most of the key agronomic traits, including yield traits and plant architecture traits, are quantitative. Fine mapping of genes/ quantitative trait loci (QTL) influencing a key trait is essential for marker-assisted selection (MAS) in maize breeding. However, the SNP markers with high density and high polymorphism are lacking, especially kompetitive allele specific PCR (KASP) SNP markers that can be used for automatic genotyping. To date, a large volume of sequencing data has been produced by the next generation sequencing technology, which provides a good pool of SNP loci for development of SNP markers. In this study, we carried out a multi-step screening method to identify kompetitive allele specific PCR (KASP) SNP markers based on the RNA-Seq data sets of 368 maize inbred lines. Results: A total of 2,948,985 SNPs were identified in the high-throughput RNA-Seq data sets with the average density of 1.4 SNP/kb. Of these, 71,311 KASP SNP markers (the average density of 34 KASP SNP/Mb) were developed based on the strict criteria: unique genomic region, bi-allelic, polymorphism information content (PIC) value ≥0.4, and conserved primer sequences, and were mapped on 16,161 genes. These 16,161 genes were annotated to 52 gene ontology (GO) terms, including most of primary and secondary metabolic pathways. Subsequently, the 50 KASP SNP markers with the PIC values ranging from 0.14 to 0.5 in 368 RNA-Seq data sets and with polymorphism between the maize inbred lines 1212 and B73 in in silico analysis were selected to experimentally validate the accuracy and polymorphism of SNPs, resulted in 46 SNPs (92.00%) showed polymorphism between the maize inbred lines 1212 and B73. Moreover, these 46 polymorphic SNPs were utilized to genotype the other 20 maize inbred lines, with all 46 SNPs showing polymorphism in the 20 maize inbred lines, and the PIC value of each SNP was 0.11 to 0.50 with an average of 0.35. The results suggested that the KASP SNP markers developed in this study were accurate and polymorphic. Conclusions: These high-density polymorphic KASP SNP markers will be a valuable resource for map-based cloning of QTL/genes and marker-assisted selection in maize. Furthermore, the method used to develop SNP markers in maize can also be applied in other species.
546			_aText in English
650		7	_aMaize _gAGROVOC _2 _91173
650		0	_aSingle nucleotide polymorphisms _gAGROVOC _910805
650		0	_aPolymorphism _gAGROVOC _93752
650		7	_2AGROVOC _91848 _aGenetic markers
650		7	_2AGROVOC _99041 _aRNA Sequence
700	0		_919714 _aDengguo Tang
700	0		_919715 _aJixing Ni
700	0		_916625 _aLi Peng
700	0		_919716 _aLe Wang
700	0		_919717 _aJinhong Zhou
700	0		_919718 _aChenyang Li
700	0		_96533 _aHai Lan
700	0		_919719 _aLujiang Li
700	0		_919720 _aJian Liu
773	0		_tBMC Plant Biology _gv. 21, art. 157 _dLondon (United Kingdom) : BioMed Central, 2021. _x1471-2229 _wGu79387
856	4		_yClick here to access online _uhttps://doi.org/10.1186/s12870-021-02932-8
942			_cJA _n0 _2ddc