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Title: Resequencing of cv CRI-12 family reveals haplotype block inheritance and recombination of agronomically important genes in artificial selection

Author
item LU, XUKE - Chinese Academy Of Agricultural Sciences
item FU, XIAOQIONG - Chinese Academy Of Agricultural Sciences
item WANG, DELONG - Chinese Academy Of Agricultural Sciences
item WANG, JUNYI - Hangzhou 1gene Technology Co, Ltd
item CHEN, XIUGUI - Chinese Academy Of Agricultural Sciences
item HAO, MEIRONG - Hangzhou 1gene Technology Co, Ltd
item WANG, JUNJUAN - Chinese Academy Of Agricultural Sciences
item GERVERS, KYLE - Texas A&M University
item GUO, LIXUE - Chinese Academy Of Agricultural Sciences
item WANG, SHUI - Chinese Academy Of Agricultural Sciences
item YIN, ZUJUN - Chinese Academy Of Agricultural Sciences
item FAN, WEILI - Chinese Academy Of Agricultural Sciences
item SHI, CHUNWEI - Hangzhou 1gene Technology Co, Ltd
item WANG, XIAOGE - Chinese Academy Of Agricultural Sciences
item PENG, JUN - Chinese Academy Of Agricultural Sciences
item CHEN, CHAO - Chinese Academy Of Agricultural Sciences
item CUI, RUIFENG - Chinese Academy Of Agricultural Sciences
item SHU, NA - Chinese Academy Of Agricultural Sciences
item ZHANG, BINGLEI - Chinese Academy Of Agricultural Sciences
item HAN, MINGGE - Chinese Academy Of Agricultural Sciences
item ZHAO, XIAOJIE - Chinese Academy Of Agricultural Sciences
item MU, MIN - Chinese Academy Of Agricultural Sciences
item Yu, John
item YE, WUWEI - Chinese Academy Of Agricultural Sciences

Submitted to: Plant Biotechnology Journal
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/22/2018
Publication Date: 5/1/2019
Citation: Lu, X., Fu, X., Wang, D., Wang, J., Chen, X., Hao, M., Wang, J., Gervers, K.A., Guo, L., Wang, S., Yin, Z., Fan, W., Shi, C., Wang, X., Peng, J., Chen, C., Cui, R., Shu, N., Zhang, B., Han, M., Zhao, X., Mu, M., Yu, J., Ye, W. 2019. Resequencing of cv CRI-12 family reveals haplotype block inheritance and recombination of agronomically important genes in artificial selection. Plant Biotechnology Journal. 17(5):945-955. https://doi.org/10.1111/pbi.13030.
DOI: https://doi.org/10.1111/pbi.13030

Interpretive Summary: Understanding the genetic variation of Upland cotton pedigrees is essential in exploiting beneficial genes for cotton improvement. However, characterization of significant variants inherited through the cotton breeding process has been very challenging, with limited progress thus far. With the recent completion of genome sequence for Upland cotton genetic standard Texas Marker -1 (TM-1), we are able to re-sequence a most cultivated Upland cotton (CRI-12) and its family (parents and progeny). In this re-sequencing study we developed 3.3 million DNA markers called single nucleotide polymorphism (SNP) markers. We then discovered a total of 58,116 genomic blocks, of which 23,752 are likely inherited and 1,029 recombined under artificial selection. We successfully identified 118, 126 and 176 genes that improve the resistance, respectively, to biotic (Verticillium wilt), and abiotic (salinity and drought) stress. Among many benefits including gene discovery for agronomic traits, the results from this study shed light on the genetic mechanism of artificial selection during the breeding process. The new knowledge will help guide future breeding efforts to more effectively improve cotton as well as other crop plants.

Technical Abstract: Although efforts have been taken to exploit diversity for yield and quality improvements, limited progress has been made with using beneficial alleles in domesticated and undomesticated varieties in cotton breeding. Given the complexity and limited amount of the genome described to date since the completion of the diploid genomes of Gossypium arboretum (AA) and G. raimondii (DD), and the allotetraploid G. hirsutum (AtDt) genome, characterizing significant variations inherited via the cotton breeding process has been challenging. Here we sequenced G. hirsutum L.cv CRI-12 (the cotton variety with the largest acreage in the world), its parental cultivars, and progeny cultivars, which were bred by the different institutes from Chinese institutions. In total, 3.3 million SNPs were identified and 118, 126 and 176 genes with increased expression were found respectively correlating with Verticillium dahlia, salinity and drought resistance in CRI-12. Transcriptome-wide analyses of gene expression, along with functional annotations, have provided support for the identification of genes tied to these resistances. We totally discovered 58,116 haplotype blocks, among which 23,752 may be inherited and 1,029 may be recombined under artificial selection. This survey of genetic diversity identified loci that may have been subject to artificial selection and documented the haplotype inheritance and recombination, shedding light on the genetic mechanism of artificial selection and guiding breeding efforts across the world for the genetic improvement of cotton.