Development of genic KASP SNP markers from RNA-Seq data for map-based cloning and marker-assisted selection in maize (Record no. 63661)
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| 000 -LEADER | |
|---|---|
| fixed length control field | 03784nab|a22004217a|4500 |
| 001 - CONTROL NUMBER | |
| control field | 63661 |
| 003 - CONTROL NUMBER IDENTIFIER | |
| control field | MX-TxCIM |
| 005 - DATE AND TIME OF LATEST TRANSACTION | |
| control field | 20240826225837.0 |
| 008 - FIXED-LENGTH DATA ELEMENTS--GENERAL INFORMATION | |
| fixed length control field | 200910s2021||||xxk|||p|op||||00||0|eng|d |
| 022 ## - INTERNATIONAL STANDARD SERIAL NUMBER | |
| International Standard Serial Number | 1471-2229 |
| 024 8# - OTHER STANDARD IDENTIFIER | |
| Standard number or code | https://doi.org/10.1186/s12870-021-02932-8 |
| 040 ## - CATALOGING SOURCE | |
| Original cataloging agency | MX-TxCIM |
| 041 ## - LANGUAGE CODE | |
| Language code of text/sound track or separate title | eng |
| 100 0# - MAIN ENTRY--PERSONAL NAME | |
| Personal name | Zhengjie Chen |
| 9 (RLIN) | 19713 |
| 245 10 - TITLE STATEMENT | |
| Title | Development of genic KASP SNP markers from RNA-Seq data for map-based cloning and marker-assisted selection in maize |
| 260 ## - PUBLICATION, DISTRIBUTION, ETC. (IMPRINT) | |
| Place of publication, distribution, etc. | London (United Kingdom) : |
| Name of publisher, distributor, etc. | BioMed Central, |
| Date of publication, distribution, etc. | 2021. |
| 500 ## - GENERAL NOTE | |
| General note | Peer review |
| 500 ## - GENERAL NOTE | |
| General note | Open Access |
| 520 ## - SUMMARY, ETC. | |
| Summary, etc. | Background: 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 ## - LANGUAGE NOTE | |
| Language note | Text in English |
| 650 #7 - SUBJECT ADDED ENTRY--TOPICAL TERM | |
| Topical term or geographic name as entry element | Maize |
| Miscellaneous information | AGROVOC |
| Source of heading or term | |
| 9 (RLIN) | 1173 |
| 650 #0 - SUBJECT ADDED ENTRY--TOPICAL TERM | |
| Topical term or geographic name as entry element | Single nucleotide polymorphisms |
| Miscellaneous information | AGROVOC |
| 9 (RLIN) | 10805 |
| 650 #0 - SUBJECT ADDED ENTRY--TOPICAL TERM | |
| Topical term or geographic name as entry element | Polymorphism |
| Miscellaneous information | AGROVOC |
| 9 (RLIN) | 3752 |
| 650 #7 - SUBJECT ADDED ENTRY--TOPICAL TERM | |
| Source of heading or term | AGROVOC |
| 9 (RLIN) | 1848 |
| Topical term or geographic name as entry element | Genetic markers |
| 650 #7 - SUBJECT ADDED ENTRY--TOPICAL TERM | |
| Source of heading or term | AGROVOC |
| 9 (RLIN) | 9041 |
| Topical term or geographic name as entry element | RNA Sequence |
| 700 0# - ADDED ENTRY--PERSONAL NAME | |
| 9 (RLIN) | 19714 |
| Personal name | Dengguo Tang |
| 700 0# - ADDED ENTRY--PERSONAL NAME | |
| 9 (RLIN) | 19715 |
| Personal name | Jixing Ni |
| 700 0# - ADDED ENTRY--PERSONAL NAME | |
| 9 (RLIN) | 16625 |
| Personal name | Li Peng |
| 700 0# - ADDED ENTRY--PERSONAL NAME | |
| 9 (RLIN) | 19716 |
| Personal name | Le Wang |
| 700 0# - ADDED ENTRY--PERSONAL NAME | |
| 9 (RLIN) | 19717 |
| Personal name | Jinhong Zhou |
| 700 0# - ADDED ENTRY--PERSONAL NAME | |
| 9 (RLIN) | 19718 |
| Personal name | Chenyang Li |
| 700 0# - ADDED ENTRY--PERSONAL NAME | |
| 9 (RLIN) | 6533 |
| Personal name | Hai Lan |
| 700 0# - ADDED ENTRY--PERSONAL NAME | |
| 9 (RLIN) | 19719 |
| Personal name | Lujiang Li |
| 700 0# - ADDED ENTRY--PERSONAL NAME | |
| 9 (RLIN) | 19720 |
| Personal name | Jian Liu |
| 773 0# - HOST ITEM ENTRY | |
| Title | BMC Plant Biology |
| Related parts | v. 21, art. 157 |
| Place, publisher, and date of publication | London (United Kingdom) : BioMed Central, 2021. |
| International Standard Serial Number | 1471-2229 |
| Record control number | Gu79387 |
| 856 4# - ELECTRONIC LOCATION AND ACCESS | |
| Link text | Click here to access online |
| Uniform Resource Identifier | https://doi.org/10.1186/s12870-021-02932-8 |
| 942 ## - ADDED ENTRY ELEMENTS (KOHA) | |
| Koha item type | Article |
| Suppress in OPAC | No |
| Source of classification or shelving scheme | Dewey Decimal Classification |
| Date last seen | Total Checkouts | Price effective from | Koha item type | Lost status | Source of classification or shelving scheme | Damaged status | Not for loan | Collection code | Withdrawn status | Home library | Current library | Date acquired |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 05/03/2021 | 05/03/2021 | Article | Not Lost | Dewey Decimal Classification | Reprints Collection | CIMMYT Knowledge Center: John Woolston Library | CIMMYT Knowledge Center: John Woolston Library | 05/03/2021 |