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| Status |
Public on Jan 08, 2023 |
| Title |
Mapping quantitative trait loci and developing their KASP markers for Pre-harvest Sprouting resistance of Henan wheat varieties in China |
| Organism |
Triticum aestivum |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Introduction: Pre-harvest Sprouting (PHS) seriously affects wheat quality and yield. However, to date there have been limited reports. It is of great urgency to breed resistance varieties via quantitative trait nucleotides (QTNs) or genes for PHS resistance in white-grained wheat. Methods: 629 Chinese wheat varieties, including 373 local wheat varieties from 70 years ago and 256 improved wheat varieties were phenotyped for spike sprouting (SS) in two environments and genotyped by wheat 660K microarray. These phenotypes were used to associate with 314,548 SNP markers for identifying QTNs for PHS resistance using several multi-locus genome-wide association study (GWAS) methods. Their candidate genes were verified by RNA-seq, and the validated candidate genes were further exploited in wheat breeding. Results: As a result, variation coefficients of 50% and 47% for PHS in 629 wheat varieties, respectively, in 2020-2021 and 2021-2022 indicated large phenotypic variation, in particular, 38 white grain varieties appeared at least medium resistance, such as Baipimai, Fengchan 3, and Jimai 20. In GWAS, 22 significant QTNs, with the sizes of 0.06% ~ 38.11%, for PHS resistance were stably identified by multiple multi-locus methods in two environments, e.g., AX-95124645 (chr3D:571.35Mb), with the sizes of 36.390% and 45.850% in 2020-2021 and 2021-2022, respectively, was detected by several multi-locus methods in two environments. As compared with previous studies, the AX-95124645 was used to develop Kompetitive Allele-Specific PCR marker QSS.TAF9-3D (chr3D:569.17Mb~573.55Mb) for the first time, especially, it is available in white-grain wheat varieties. Around this locus, nine genes were significantly differentially expressed, and two of them (TraesCS3D01G466100 and TraesCS3D01G468500) were found by GO annotation to be related to PHS resistance and determined as candidate genes. Discussion: The QTN and two new candidate genes related to PHS resistance were identified in this study. The QTN can be used to effectively identify the PHS resistance materials, especially, all the white-grained varieties with QSS.TAF9-3D-TT haplotype are resistant to spike sprouting. Thus, this study provides candidate genes, materials, and methodological basis for breeding wheat PHS resistance in the future.
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| Overall design |
Spike of wheat wax ripe stage
Time: 0 hour, 48hour and 96 hour represents the time the sample was processed at a temperature of 22 plus or minus 1 degrees C and a relative humidity of 95% plus or minus 5%.
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| Contributor(s) |
Kou C, Peng C, Dong H, HU L, Xu W |
| Citation(s) |
36875573 |
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| Submission date |
Jan 06, 2023 |
| Last update date |
Jun 14, 2023 |
| Contact name |
Cheng Kou |
| E-mail(s) |
koucheng7417@outlook.com
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| Phone |
+8615290564435
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| Organization name |
Northwest A&F University
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| Street address |
3 Tai Cheng Road, Yangling District, Xianyang City, Shaanxi Province, China
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| City |
Xianyang |
| ZIP/Postal code |
712100 |
| Country |
China |
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| Platforms (1) |
| GPL25409 |
Illumina NovaSeq 6000 (Triticum aestivum) |
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| Samples (27)
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| GSM6921279 |
Shengsimai, 0hour, rep1 |
| GSM6921280 |
Shengsimai, 0hour, rep2 |
| GSM6921281 |
Shengsimai, 0hour, rep3 |
| GSM6921282 |
Zhoumai18, 0hour, rep1 |
| GSM6921283 |
Zhoumai18, 0hour, rep2 |
| GSM6921284 |
Zhoumai18, 0hour, rep3 |
| GSM6921285 |
Baipimai, 48hour, rep1 |
| GSM6921286 |
Baipimai, 48hour, rep2 |
| GSM6921287 |
Baipimai, 48hour, rep3 |
| GSM6921288 |
Shengsimai, 48hour, rep1 |
| GSM6921289 |
Shengsimai, 48hour, rep2 |
| GSM6921290 |
Shengsimai, 48hour, rep3 |
| GSM6921291 |
Zhoumai18, 48hour, rep1 |
| GSM6921292 |
Zhoumai18, 48hour, rep2 |
| GSM6921293 |
Zhoumai18, 48hour, rep3 |
| GSM6921294 |
Baipimai, 96hour, rep1 |
| GSM6921295 |
Baipimai, 96hour, rep2 |
| GSM6921296 |
Baipimai, 96hour, rep3 |
| GSM6921297 |
Shengsimai, 96hour, rep1 |
| GSM6921298 |
Shengsimai, 96hour, rep2 |
| GSM6921299 |
Shengsimai, 96hour, rep3 |
| GSM6921300 |
Zhoumai18, 96hour, rep1 |
| GSM6921301 |
Zhoumai18, 96hour, rep2 |
| GSM6921302 |
Zhoumai18, 96hour, rep3 |
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| Relations |
| BioProject |
PRJNA919175 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE222342_FPKM.txt.gz |
16.0 Mb |
(ftp)(http) |
TXT |
| GSE222342_Phenotype_data_of_the_cultivars.txt.gz |
262 b |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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