Taxus cuspidata is a rare plant with important medicinal and ornamental value.Aiming at the obvious differences between wild and cultivated populations of T.cuspidata from Northeast China,a total of 61 samples,that is...Taxus cuspidata is a rare plant with important medicinal and ornamental value.Aiming at the obvious differences between wild and cultivated populations of T.cuspidata from Northeast China,a total of 61 samples,that is,33 wild yews and 28 cultivated yews were used to analyze the differences and correlations of the kinship,genetic diversity,and genetic structure between them by specific length amplified fragment sequencing(SLAF-seq).Finally,470725 polymorphic SLAF tags and 58622 valid SNP markers were obtained.Phylogenetic analysis showed that 61 samples were classified into 2 clusters:wild populations and cultivated populations,and some wild yews were categorized into the cultivated populations;the genetic diversity analysis showed that the Nei diversity index of wild populations(0.4068)was smaller than that of cultivated populations(0.4414),and the polymorphic information content(PIC)of wild populations(0.2861)was smaller than that of cultivated populations(0.3309).The genetic differentiation analysis showed that the total populations of gene diversity(H_(t))of cultivated and wild populations were respectively 0.8159 and 0.5685,the coefficient of gene differentiation(G_(st))of cultivated and wild populations was respectively 0.3021 and 0.1068,and the gene flow(N_(m))(2.4967)of wild populations was larger than cultivated populations(0.8199).The molecular variance(AMOVA)revealed that inter-population variation accounted for 29.57%of the total genetic variation,while intra-population variation accounted for 70.42% of the total genetic variation(p<0.001),this suggested that the genetic variation in the T.cuspidata is mainly attributed to within-population factors.In conclusion,the genetic distance between geographical ecological groups of wild populations was generally smaller than that of cultivated populations,and the degree of genetic diversity and genetic differentiation was smaller than that of cultivated populations.As evident,the utilization of SLAF-seq technology enables efficient and accurate development of SNP markers suitable for genetic analysis of T.cuspidata species.These developed SNP markers can provide a molecular foundation for T.cuspidata breeding,construction of genetic maps,variety identification,and association analysis of agronomic traits.展开更多
Chinese traditional medicine Danshen is the radix of the perennial herbs of Salvia miltiorrhiza Bunge, which has a variety of pharmacological effects and is traditionally and extensively applied clinically to treat ca...Chinese traditional medicine Danshen is the radix of the perennial herbs of Salvia miltiorrhiza Bunge, which has a variety of pharmacological effects and is traditionally and extensively applied clinically to treat cardiovascular disorders. In this research, the genomic genes for tyrosine aminotransferase (TAT) of 38 cultivated populations of Danshen in China were cloned and bioinformatic analyses were conducted to reveal its genetic diversity and phylogeny. The full-length SmTAT was 2296 - 2444 bp including 6 exons (encoding 411 amino acids) and 5 introns. Overall, the SmTAT genes in cultivated Danshen populations are highly conserved with a relative low level of genetic diversity. The spliced exons (1236 bp) had 23 SNP variations with a rate of 1.86%, of which 22 occurred in the white flower S. miltiorrhiza Bge.f.alba population (W-SCHY-W-1) and led to 5 amino acid variations. The entire 290 SNP variations with a rate of 24% in the 5 introns occurred exclusively in W-SCHY-W-1. Phylogenetic trees based on the full-length, combined introns, the spliced exons, and the deduced amino acid sequences of SmTAT all showed a two-clade basic structure with W-SCHY-W-1 uniquely standing alone. The SmTAT gene of the white flower population (W-SCHY-W-1) is unique and especially rich in variations. The first time clarified genomic SmTAT gene structure and genetic diversity in cultivated Danshen populations laid an excellent foundation for further studies on the biosynthesis of bioactives and the molecular breeding of Danshen as well as in plant tyrosine metabolism.展开更多
基金This work was supported by Grants from the National Science Foundation of China to Yanwen Zhang(32272757,31972363)Grants from the Liaoning Provincial Department of Education Project to Dandan Wang(JYTMS20230698)Grants from the Liaoning Provincial Science and Technology Fund Project:Comparative Multi-Omics Study of Wild and Cultivated Species of Taxus chinensis.
文摘Taxus cuspidata is a rare plant with important medicinal and ornamental value.Aiming at the obvious differences between wild and cultivated populations of T.cuspidata from Northeast China,a total of 61 samples,that is,33 wild yews and 28 cultivated yews were used to analyze the differences and correlations of the kinship,genetic diversity,and genetic structure between them by specific length amplified fragment sequencing(SLAF-seq).Finally,470725 polymorphic SLAF tags and 58622 valid SNP markers were obtained.Phylogenetic analysis showed that 61 samples were classified into 2 clusters:wild populations and cultivated populations,and some wild yews were categorized into the cultivated populations;the genetic diversity analysis showed that the Nei diversity index of wild populations(0.4068)was smaller than that of cultivated populations(0.4414),and the polymorphic information content(PIC)of wild populations(0.2861)was smaller than that of cultivated populations(0.3309).The genetic differentiation analysis showed that the total populations of gene diversity(H_(t))of cultivated and wild populations were respectively 0.8159 and 0.5685,the coefficient of gene differentiation(G_(st))of cultivated and wild populations was respectively 0.3021 and 0.1068,and the gene flow(N_(m))(2.4967)of wild populations was larger than cultivated populations(0.8199).The molecular variance(AMOVA)revealed that inter-population variation accounted for 29.57%of the total genetic variation,while intra-population variation accounted for 70.42% of the total genetic variation(p<0.001),this suggested that the genetic variation in the T.cuspidata is mainly attributed to within-population factors.In conclusion,the genetic distance between geographical ecological groups of wild populations was generally smaller than that of cultivated populations,and the degree of genetic diversity and genetic differentiation was smaller than that of cultivated populations.As evident,the utilization of SLAF-seq technology enables efficient and accurate development of SNP markers suitable for genetic analysis of T.cuspidata species.These developed SNP markers can provide a molecular foundation for T.cuspidata breeding,construction of genetic maps,variety identification,and association analysis of agronomic traits.
文摘Chinese traditional medicine Danshen is the radix of the perennial herbs of Salvia miltiorrhiza Bunge, which has a variety of pharmacological effects and is traditionally and extensively applied clinically to treat cardiovascular disorders. In this research, the genomic genes for tyrosine aminotransferase (TAT) of 38 cultivated populations of Danshen in China were cloned and bioinformatic analyses were conducted to reveal its genetic diversity and phylogeny. The full-length SmTAT was 2296 - 2444 bp including 6 exons (encoding 411 amino acids) and 5 introns. Overall, the SmTAT genes in cultivated Danshen populations are highly conserved with a relative low level of genetic diversity. The spliced exons (1236 bp) had 23 SNP variations with a rate of 1.86%, of which 22 occurred in the white flower S. miltiorrhiza Bge.f.alba population (W-SCHY-W-1) and led to 5 amino acid variations. The entire 290 SNP variations with a rate of 24% in the 5 introns occurred exclusively in W-SCHY-W-1. Phylogenetic trees based on the full-length, combined introns, the spliced exons, and the deduced amino acid sequences of SmTAT all showed a two-clade basic structure with W-SCHY-W-1 uniquely standing alone. The SmTAT gene of the white flower population (W-SCHY-W-1) is unique and especially rich in variations. The first time clarified genomic SmTAT gene structure and genetic diversity in cultivated Danshen populations laid an excellent foundation for further studies on the biosynthesis of bioactives and the molecular breeding of Danshen as well as in plant tyrosine metabolism.
