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Genome-wide high-throughput SNP discovery and genotyping for understanding natural (functional) allelic diversity and domestication patterns in wild chickpea.

Bajaj D, Das S, Badoni S, Kumar V, Singh M, Bansal KC, Tyagi AK, Parida SK - Sci Rep (2015)

Bottom Line: We identified 82489 high-quality genome-wide SNPs from 93 wild and cultivated Cicer accessions through integrated reference genome- and de novo-based GBS assays.The functional significance of allelic variants (non-synonymous and regulatory SNPs) scanned from transcription factors and stress-responsive genes in differentiating wild accessions (with potential known sources of yield-contributing and stress tolerance traits) from cultivated desi and kabuli accessions, fine-mapping/map-based cloning of QTLs and determination of LD patterns across wild and cultivated gene-pools are suitably elucidated.The correlation between phenotypic (agromorphological traits) and molecular diversity-based admixed domestication patterns within six structured populations of wild and cultivated accessions via genome-wide SNPs was apparent.

View Article: PubMed Central - PubMed

Affiliation: National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India.

ABSTRACT
We identified 82489 high-quality genome-wide SNPs from 93 wild and cultivated Cicer accessions through integrated reference genome- and de novo-based GBS assays. High intra- and inter-specific polymorphic potential (66-85%) and broader natural allelic diversity (6-64%) detected by genome-wide SNPs among accessions signify their efficacy for monitoring introgression and transferring target trait-regulating genomic (gene) regions/allelic variants from wild to cultivated Cicer gene pools for genetic improvement. The population-specific assignment of wild Cicer accessions pertaining to the primary gene pool are more influenced by geographical origin/phenotypic characteristics than species/gene-pools of origination. The functional significance of allelic variants (non-synonymous and regulatory SNPs) scanned from transcription factors and stress-responsive genes in differentiating wild accessions (with potential known sources of yield-contributing and stress tolerance traits) from cultivated desi and kabuli accessions, fine-mapping/map-based cloning of QTLs and determination of LD patterns across wild and cultivated gene-pools are suitably elucidated. The correlation between phenotypic (agromorphological traits) and molecular diversity-based admixed domestication patterns within six structured populations of wild and cultivated accessions via genome-wide SNPs was apparent. This suggests utility of whole genome SNPs as a potential resource for identifying naturally selected trait-regulating genomic targets/functional allelic variants adaptive to diverse agroclimatic regions for genetic enhancement of cultivated gene-pools.

No MeSH data available.


Related in: MedlinePlus

Genome-wide SNP-based molecular diversity, phylogeny and population genetic structure among 93 wild and cultivated Cicer accessions.(A) Population genetic structure among 93 wild and cultivated accessions using 27862 genome-wide SNPs. These SNPs assigned 93 accessions into six populations (POP I, POP II, POP III, POP IV, POP V and POP VI) that majorly grouped as per their species and gene pools of origination. The accessions represented by vertical bars along the horizontal axis were classified into K colour segments based on their estimated membership fraction in each K cluster. Six diverse colours represent different population groups based on optimal population number K = 6. (B) Unrooted phylogram illustrating the genetic relationships (Nei’s genetic distance) among 93 wild and cultivated accessions belonging to seven Cicer species using 27862 genome-wide SNPs. The phylogenetic tree clearly differentiated 93 accessions into six diverse groups, which correspond to their species and gene pools of origination. (C) Principal component analysis (PCA) differentiating the 93 wild and cultivated accessions belonging to seven Cicer species into six populations (POP I, POP II, POP III, POP IV, POP V and POP VI) as determined by population genetic structure. The PC1, PC2, PC3, PC4, PC5 and PC6 explained 10.2%, 7.8%, 3.7%, 3.4%, 2.7%, 2.4% and 2.3% of the total variance, respectively.
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f2: Genome-wide SNP-based molecular diversity, phylogeny and population genetic structure among 93 wild and cultivated Cicer accessions.(A) Population genetic structure among 93 wild and cultivated accessions using 27862 genome-wide SNPs. These SNPs assigned 93 accessions into six populations (POP I, POP II, POP III, POP IV, POP V and POP VI) that majorly grouped as per their species and gene pools of origination. The accessions represented by vertical bars along the horizontal axis were classified into K colour segments based on their estimated membership fraction in each K cluster. Six diverse colours represent different population groups based on optimal population number K = 6. (B) Unrooted phylogram illustrating the genetic relationships (Nei’s genetic distance) among 93 wild and cultivated accessions belonging to seven Cicer species using 27862 genome-wide SNPs. The phylogenetic tree clearly differentiated 93 accessions into six diverse groups, which correspond to their species and gene pools of origination. (C) Principal component analysis (PCA) differentiating the 93 wild and cultivated accessions belonging to seven Cicer species into six populations (POP I, POP II, POP III, POP IV, POP V and POP VI) as determined by population genetic structure. The PC1, PC2, PC3, PC4, PC5 and PC6 explained 10.2%, 7.8%, 3.7%, 3.4%, 2.7%, 2.4% and 2.3% of the total variance, respectively.

Mentions: The determination of the population genetic structure among 93 wild and cultivated Cicer accessions using 27862 genome-wide SNPs at varying levels of possible population numbers (K = 1 to 10) with 20 replications revealed the most apparent inflection of average LnP(D) (log-likelihood) at one of the best replicates of K = 6. The population numbers (K) were further validated using the second order statistics of STRUCTURE by ΔK estimation. Overall, these analyses support the classification of 93 accessions into six distinct populations (POP I–VI) with a high-resolution population structure (Fig. 2A). POP I consisted of 12 cultivated desi and kabuli accessions of C. arietinum. POP II consisted of 24 wild accessions from C. reticulatum (16) and C. echinospermum (8). POP III, IV, V and VI included accessions from C. judaicum (22 accessions), C. bijugum (18), C. pinnatifidum (16) and C. microphyllum (1), respectively. The high-resolution assignment of 93 accessions into six populations was comparable with their clustering patterns and phylogeny obtained by the neighbor-joining unrooted phylogram (Fig. 2B) and PCA (Fig. 2C). The classification of species/accessions representing members of primary (C. arietinum, C. reticulatum and C. echinospermum) and secondary (C. bijugum, C. pinnatifidum and C. judaicum) gene pools into six diverse populations is comparable with previous molecular diversity, population genetic structure and evolutionary studies6293638394041424445464752535455. The inclusion of accessions from wild annual Cicer species (C. reticulatum and C. echinospermum) into one population (POP II) infers that geographical origin (Turkey), including phenotypic characteristics (growth habits), rather than species/gene pools of origination had a greater impact on the clustering patterns in a wild population51.


Genome-wide high-throughput SNP discovery and genotyping for understanding natural (functional) allelic diversity and domestication patterns in wild chickpea.

Bajaj D, Das S, Badoni S, Kumar V, Singh M, Bansal KC, Tyagi AK, Parida SK - Sci Rep (2015)

Genome-wide SNP-based molecular diversity, phylogeny and population genetic structure among 93 wild and cultivated Cicer accessions.(A) Population genetic structure among 93 wild and cultivated accessions using 27862 genome-wide SNPs. These SNPs assigned 93 accessions into six populations (POP I, POP II, POP III, POP IV, POP V and POP VI) that majorly grouped as per their species and gene pools of origination. The accessions represented by vertical bars along the horizontal axis were classified into K colour segments based on their estimated membership fraction in each K cluster. Six diverse colours represent different population groups based on optimal population number K = 6. (B) Unrooted phylogram illustrating the genetic relationships (Nei’s genetic distance) among 93 wild and cultivated accessions belonging to seven Cicer species using 27862 genome-wide SNPs. The phylogenetic tree clearly differentiated 93 accessions into six diverse groups, which correspond to their species and gene pools of origination. (C) Principal component analysis (PCA) differentiating the 93 wild and cultivated accessions belonging to seven Cicer species into six populations (POP I, POP II, POP III, POP IV, POP V and POP VI) as determined by population genetic structure. The PC1, PC2, PC3, PC4, PC5 and PC6 explained 10.2%, 7.8%, 3.7%, 3.4%, 2.7%, 2.4% and 2.3% of the total variance, respectively.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4513697&req=5

f2: Genome-wide SNP-based molecular diversity, phylogeny and population genetic structure among 93 wild and cultivated Cicer accessions.(A) Population genetic structure among 93 wild and cultivated accessions using 27862 genome-wide SNPs. These SNPs assigned 93 accessions into six populations (POP I, POP II, POP III, POP IV, POP V and POP VI) that majorly grouped as per their species and gene pools of origination. The accessions represented by vertical bars along the horizontal axis were classified into K colour segments based on their estimated membership fraction in each K cluster. Six diverse colours represent different population groups based on optimal population number K = 6. (B) Unrooted phylogram illustrating the genetic relationships (Nei’s genetic distance) among 93 wild and cultivated accessions belonging to seven Cicer species using 27862 genome-wide SNPs. The phylogenetic tree clearly differentiated 93 accessions into six diverse groups, which correspond to their species and gene pools of origination. (C) Principal component analysis (PCA) differentiating the 93 wild and cultivated accessions belonging to seven Cicer species into six populations (POP I, POP II, POP III, POP IV, POP V and POP VI) as determined by population genetic structure. The PC1, PC2, PC3, PC4, PC5 and PC6 explained 10.2%, 7.8%, 3.7%, 3.4%, 2.7%, 2.4% and 2.3% of the total variance, respectively.
Mentions: The determination of the population genetic structure among 93 wild and cultivated Cicer accessions using 27862 genome-wide SNPs at varying levels of possible population numbers (K = 1 to 10) with 20 replications revealed the most apparent inflection of average LnP(D) (log-likelihood) at one of the best replicates of K = 6. The population numbers (K) were further validated using the second order statistics of STRUCTURE by ΔK estimation. Overall, these analyses support the classification of 93 accessions into six distinct populations (POP I–VI) with a high-resolution population structure (Fig. 2A). POP I consisted of 12 cultivated desi and kabuli accessions of C. arietinum. POP II consisted of 24 wild accessions from C. reticulatum (16) and C. echinospermum (8). POP III, IV, V and VI included accessions from C. judaicum (22 accessions), C. bijugum (18), C. pinnatifidum (16) and C. microphyllum (1), respectively. The high-resolution assignment of 93 accessions into six populations was comparable with their clustering patterns and phylogeny obtained by the neighbor-joining unrooted phylogram (Fig. 2B) and PCA (Fig. 2C). The classification of species/accessions representing members of primary (C. arietinum, C. reticulatum and C. echinospermum) and secondary (C. bijugum, C. pinnatifidum and C. judaicum) gene pools into six diverse populations is comparable with previous molecular diversity, population genetic structure and evolutionary studies6293638394041424445464752535455. The inclusion of accessions from wild annual Cicer species (C. reticulatum and C. echinospermum) into one population (POP II) infers that geographical origin (Turkey), including phenotypic characteristics (growth habits), rather than species/gene pools of origination had a greater impact on the clustering patterns in a wild population51.

Bottom Line: We identified 82489 high-quality genome-wide SNPs from 93 wild and cultivated Cicer accessions through integrated reference genome- and de novo-based GBS assays.The functional significance of allelic variants (non-synonymous and regulatory SNPs) scanned from transcription factors and stress-responsive genes in differentiating wild accessions (with potential known sources of yield-contributing and stress tolerance traits) from cultivated desi and kabuli accessions, fine-mapping/map-based cloning of QTLs and determination of LD patterns across wild and cultivated gene-pools are suitably elucidated.The correlation between phenotypic (agromorphological traits) and molecular diversity-based admixed domestication patterns within six structured populations of wild and cultivated accessions via genome-wide SNPs was apparent.

View Article: PubMed Central - PubMed

Affiliation: National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India.

ABSTRACT
We identified 82489 high-quality genome-wide SNPs from 93 wild and cultivated Cicer accessions through integrated reference genome- and de novo-based GBS assays. High intra- and inter-specific polymorphic potential (66-85%) and broader natural allelic diversity (6-64%) detected by genome-wide SNPs among accessions signify their efficacy for monitoring introgression and transferring target trait-regulating genomic (gene) regions/allelic variants from wild to cultivated Cicer gene pools for genetic improvement. The population-specific assignment of wild Cicer accessions pertaining to the primary gene pool are more influenced by geographical origin/phenotypic characteristics than species/gene-pools of origination. The functional significance of allelic variants (non-synonymous and regulatory SNPs) scanned from transcription factors and stress-responsive genes in differentiating wild accessions (with potential known sources of yield-contributing and stress tolerance traits) from cultivated desi and kabuli accessions, fine-mapping/map-based cloning of QTLs and determination of LD patterns across wild and cultivated gene-pools are suitably elucidated. The correlation between phenotypic (agromorphological traits) and molecular diversity-based admixed domestication patterns within six structured populations of wild and cultivated accessions via genome-wide SNPs was apparent. This suggests utility of whole genome SNPs as a potential resource for identifying naturally selected trait-regulating genomic targets/functional allelic variants adaptive to diverse agroclimatic regions for genetic enhancement of cultivated gene-pools.

No MeSH data available.


Related in: MedlinePlus