Design and application of the HbGBTS80K liquid chip in rubber tree
2024
Jinquan Chao | Yan Li | Shuguang Yang | Xingming Chen | Yilin He | Jianan Zhang | Zongliang Yue | Qiang Gao | Weimin Tian
The single nucleotide polymorphism (SNP) chip provides a convenient platform for accelerating breeding progress and promoting basic research in the field of crop science. Given the long and inefficient traditional breeding of the rubber tree, it is urgent to develop an SNP chip to promote changes in breeding patterns. Here, we developed and validated a liquid SNP chip named 'HbGBTS80K'. The SNPs were selected from whole-genome resequencing data containing 335 diverse rubber tree accessions. After quality control of 69 additional accessions, the final SNP chip included 80,080 SNPs evenly distributed across 18 chromosomes. Population genetic diversity analysis showed that the HbGBTS80K was effective in distinguishing rubber accessions into four groups, which was highly consistent with previous findings based on resequencing data. Genome-wide association study (GWAS) on the reported genotypic data of the number of laticifer rings (NLR) could also detect the major gene HbPSK5 in the HbGBTS80K platform. In summary, the HbGBTS80K liquid SNP chip is a valuable tool that will facilitate functional studies and molecular breeding of the rubber tree.
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