Resolving population structure and genetic differentiation associated with RAD-SNP loci under selection in tossa jute (Corchorus olitorius L.)

et al. 2019

BMC Genomics

BackgroundSingle nucleotide polymorphisms (SNPs) and insertions/deletions (InDels) are the major genetic variations and are distributed extensively across the whole plant genome. However, few studies of these variations have been conducted in the long-lived perennial tea plant.ResultsIn this study, we investigated the genome-wide genetic variations between Camellia sinensis var. sinensis ‘Shuchazao’ and Camellia sinensis var. assamica ‘Yunkang 10’, identified 7,511,731 SNPs and 255,218 InDels based on their whole genome sequences, and we subsequently analyzed their distinct types and distribution patterns. A total of 48 InDel markers that yielded polymorphic and unambiguous fragments were developed when screening six tea cultivars. These markers were further deployed on 46 tea cultivars for transferability and genetic diversity analysis, exhibiting information with an average 4.02 of the number of alleles (Na) and 0.457 of polymorphism information content (PIC). The dendrogram showed that the phylogenetic relationships among these tea cultivars are highly consistent with their genetic backgrounds or original places. Interestingly, we observed that the catechin/caffeine contents between ‘Shuchazao’ and ‘Yunkang 10’ were significantly different, and a large number of SNPs/InDels were identified within catechin/caffeine biosynthesis-related genes.ConclusionThe identified genome-wide genetic variations and newly-developed InDel markers will provide a valuable resource for tea plant genetic and genomic studies, especially the SNPs/InDels within catechin/caffeine biosynthesis-related genes, which may serve as pivotal candidates for elucidating the molecular mechanism governing catechin/caffeine biosynthesis.

Section: Introductionmentioning

confidence: 99%

Characterization of genome-wide genetic variations between two varieties of tea plant (Camellia sinensis) and development of InDel markers for genetic research

et al. 2019

BMC Genomics

“…InDel markers have practical value for those laboratories with limited resources, which also showed reliable transferability between distinct populations [14,17,18]. Both SNPs and InDels have been extensively applied for breeding programs and genetic studies including pedigree analysis, origin and evolutionary analysis, population structure and diversity analysis, construction of linkage maps, QTL mapping, and marker-assisted selection [14,[19][20][21][22]. Several studies have also reported the development and application of SNP/InDel markers in tea plant genetic studies.…”

Section: Introductionmentioning

confidence: 99%

Characterization of genome-wide genetic variations between two varieties of tea plant (Camellia sinensis) and development of InDel markers for genetic research

et al. 2019

Preprint

Background: Single nucleotide polymorphisms (SNPs) and insertions/deletions (InDels) are the major genetic variations and are distributed extensively across the whole plant genome. However, few studies of these variations have been conducted in the long-lived perennial tea plant. Results: In this study, we investigated the genome-wide genetic variations between Camellia sinensis var. sinensis ‘Shuchazao’ and Camellia sinensis var. assamica ‘Yunkang 10’, identified 7,511,731 SNPs and 255,218 InDels based on their whole genome sequences, and we subsequently analyzed their distinct types and distribution patterns. A total of 48 InDel markers that yielded polymorphic and unambiguous fragments were developed when screening six tea cultivars. These markers were further deployed on forty-six tea cultivars for transferability and genetic diversity analysis, exhibiting information with an average 4.02 of the number of alleles (Na) and 0.457 of polymorphism information content (PIC). The dendrogram showed that the phylogenetic relationships among these tea cultivars are highly consistent with their genetic backgrounds or original places. Interestingly, we observed that the catechin/caffeine contents between ‘Shuchazao’ and ‘Yunkang 10’ were significantly different, and a large number of SNPs/InDels were identified within catechin/caffeine biosynthesis-related genes. Conclusion: The identified genome-wide genetic variations and newly-developed InDel markers will provide a valuable resource for tea plant genetic and genomic studies, especially the SNPs/InDels within catechin/caffeine biosynthesis-related genes, which may serve as pivotal candidates for elucidating the molecular mechanism governing catechin/caffeine biosynthesis.

“…Population structure analysis and phylogenetic trees can reflect the genetic diversity, pedigree relationships, and the geographic distances among plant species and/or varieties [2,16,22]. They can also be used to evaluate the reliability of molecular markers.…”

Section: Development and Application Of Indel Markersmentioning

confidence: 99%

“…InDel markers have practical value for those laboratories with limited resources, which also showed reliable transferability between distinct populations [14, 17,18]. Both SNPs and InDels have been extensively applied for breeding programs and genetic researches including pedigree analysis, origin and evolutionary analysis, population structure and diversity analysis, linkage and QTL mapping, and marker-assisted selection [14,[19][20][21][22]. Several studies have also reported the development and application of SNP/InDel markers in tea plant genetics and genomics studies.…”

Section: Introductionmentioning

confidence: 99%

Characterization of genome-wide genetic variation between two varieties of tea plant (Camellia sinensis) and development of InDel markers for genetics research

et al. 2019

Preprint

Single nucleotide polymorphisms (SNPs) and Insertions/Deletions (InDels) are the major genetic variations and distributed extensively across the plant whole genome. Few investigations of these variations, however, have been performed in the long-lived perennial tea plant. Here, we have investigated the genome-wide genetic variation between Camellia sinensis var. sinensis ‘Shuchazao’ and Camellia sinensis var. assamica ‘Yunkang 10’, generating 7,511,731 SNPs and 255,218 InDels based on their whole genome sequences, and subsequently analyzed their distinct types and distribution patterns. A total of 48 InDel markers that yielded polymorphic and unambiguous fragments were developed when screening six tea cultivars. These markers were further deployed on forty-six tea cultivars for transferability and genetic diversity analysis, exhibiting informative with an average 4.02 of the number of alleles ( Na ) and 0.457 of polymorphism information content (PIC). The dendrogram showed that the phylogenetic relationships among these tea cultivars are highly consistent with their genetic backgrounds or original places. Interestingly, we observed that the content of catechin/caffeine between ‘Shuchazao’ and ‘Yunkang 10’ were significantly different, and a large number of SNPs/InDels were identified within catechin/caffeine biosynthesis-related genes. The identified genome-wide genetic variation and newly-developed InDel markers will provide a valuable resource for tea plant genetics and genomics studies, especially those SNPs/InDels within catechin/caffeine biosynthesis-related genes can be served as pivotal candidates for elucidating the molecular mechanism of catechin/caffeine biosynthesis.