基于SLAF-seq的华山松球果数量性状全基因组关联分析

Genome-wide Association Study of the Cone Number Character in Pinus armandii Based on SLAF-seq

【目的】挖掘与华山松球果数量相关的基因。【方法】以华山松球果数量性状表型数据筛选华山松高、低球果数量单株,利用前期已开发的单核苷酸多态性(single-nucleotide polymorphism,SNP)标记结合表型数据进行全基因组关联分析(genome-wide association study,GWAS),构建华山松样品的系统发育树,发掘与华山松球果数量性状相关的SNP标记与候选基因,并进一步分析筛选出的基因在华山松针叶、木质部、韧皮部、树皮、幼嫩球果和树根的qPCR基因组织特异性表达。【结果】系统发育树显示:同一种源的单株基本处于相近的位置,而来自巍山的单株广泛分布于各个群体中,与主成分分析结果基本一致。全基因组关联分析共检测到12个与球果数量显著关联的SNP位点,其中,Marker193307的序列与纤维素合成相关基因Korrigan (KOR1,编码跨膜内切β-1,4-D葡聚糖酶)的序列相似度较高(74.74%)。qPCR基因组织特异性表达分析结果显示:该基因在华山松枝条韧皮部的表达量最高,幼嫩球果中次之,在根系的表达量最少,初步判断该基因与球果数量相关。【结论】华山松种源地相近的单株基本处于相近的位置。巍山种源的材料较其他种源拥有较为广泛的遗传变异。GWAS分析仅检索到1个与植物纤维素合成相关的基因(KOR1),该基因可能参与球果数量性状的表达。

[Purpose]To excavate genes related to the number of cones in Pinus armandii.[Methods]Based on the phenotypic data of cone number of P.armandii,the high and low cone number individual plants were screened.Combined with phenotypic data,single-nucleotide polymorphism(SNP)markers developed previously were used to genome-wide association study(GWAS),and the phylogenetic tree of P.armandii samples was constructed,the SNP markers and candidate genes related to cone number of P.armandii were excavated,and the tissue-specific expression of qPCR gene was further analyzed in six parts of P.armandii,such as needles,xylem,phloem,bark,young cones and roots.[Results]The phylogenetic tree showed that the individual plants of the same provenance were basically in a similar position,while the individual plants from Weishan were widely distributed in each population,which was basically consistent with the results of principal component analysis.A total of 12 SNP loci significantly associated with cone number were detected by GWAS.It was found that the sequence of Marker193307 was highly similar to the cellulose synthesis related gene Korrigan(KOR1,encoding transmembrane endo-β-1,4-D glucanase)(74.74%).The tissue-specific expression of qPCR results showed that the expression level of the gene was the highest in the phloem of branches,followed by the young cones,and the least in the roots.It was preliminarily judged that the gene was related to the number of cones.[Conclusion]P.armandii provenance close to the individual basically in a similar position.The materials of Weishan provenance have more extensive genetic variation than other provenances.GWAS only retrieves one gene(KOR1)related to plant cellulose synthesis,which may be involved in the expression of cone number.