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An integrated genomic approach for rapid delineation of candidate genes regulating agro-morphological traits in chickpea.

Saxena MS, Bajaj D, Das S, Kujur A, Kumar V, Singh M, Bansal KC, Tyagi AK, Parida SK - DNA Res. (2014)

Bottom Line: Most of these QTLs showed positive additive gene effects with effective allelic contribution from ICC 4958, particularly for increasing seed weight (SW) and pod and branch number.This enabled to delineate a strong SW-regulating ABI3VP1 transcription factor (TF) gene at trait-specific QTL interval and consequently identified favourable natural allelic variants and superior high seed weight-specific haplotypes in the upstream regulatory region of this gene showing increased transcript expression during seed development.The genes (TFs) harbouring diverse trait-regulating QTLs, once validated and fine-mapped by our developed rapid integrated genomic approach and through gene/QTL map-based cloning, can be utilized as potential candidates for marker-assisted genetic enhancement of chickpea.

View Article: PubMed Central - PubMed

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

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Nineteen genomic regions harbouring 27 significant QTLs (15.6–39.8% R2) associated with SW, NP, NB and PH were identified and mapped on eight LGs (LOD > 4.0 at P < 0.05) using a 229 RIL mapping population (ICC 4958 × ICC 17160) of chickpea. The genetic distance (cM) and identity of the marker loci integrated on the chromosomes are indicated on the left and right sides of the LGs, respectively. The 15 major and robust QTLs are marked with yellow boxes. The marker pairs flanking the QTLs are coloured with red and blue. Blue, violet, green and brown lines indicate the QTLs regulating SW, NB, NP and PH mapped on eight LGs. The direction of QTLs (additive effects) are designated with empty (ICC 17160-specific alleles) vs. filled (ICC 4958-specific alleles) boxes. *qSW2.1, qSW4.1, qNP8.1 and qNB1.2 correspond to known QTLs from previous studies by Cobos et al.,53,54 Hossain et al.,55 Varshney et al.56 and Gowda et al.57 This figure appears in colour in the online version of DNA Research.
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DSU031F1: Nineteen genomic regions harbouring 27 significant QTLs (15.6–39.8% R2) associated with SW, NP, NB and PH were identified and mapped on eight LGs (LOD > 4.0 at P < 0.05) using a 229 RIL mapping population (ICC 4958 × ICC 17160) of chickpea. The genetic distance (cM) and identity of the marker loci integrated on the chromosomes are indicated on the left and right sides of the LGs, respectively. The 15 major and robust QTLs are marked with yellow boxes. The marker pairs flanking the QTLs are coloured with red and blue. Blue, violet, green and brown lines indicate the QTLs regulating SW, NB, NP and PH mapped on eight LGs. The direction of QTLs (additive effects) are designated with empty (ICC 17160-specific alleles) vs. filled (ICC 4958-specific alleles) boxes. *qSW2.1, qSW4.1, qNP8.1 and qNB1.2 correspond to known QTLs from previous studies by Cobos et al.,53,54 Hossain et al.,55 Varshney et al.56 and Gowda et al.57 This figure appears in colour in the online version of DNA Research.

Mentions: A set of 839 including 470 genic and genomic SSR markers (Supplementary Fig. S2) and 369 TF gene-derived SNP markers (Supplementary Fig. S3) showing polymorphism between parental accessions were genotyped in 229 individuals of a RIL mapping population (ICC 4958 × ICC 17160) to construct an inter-specific genetic linkage map in chickpea. The linkage analysis using the markers showing significant Mendelian segregation ratio (1:1) mapped 834 markers (including 468 SSR and 366 SNP markers) on eight LGs (LG1–LG8) of chickpea (Fig. 1) according to their physical positions (bp) on respective chromosomes (Supplementary Fig. S1). The constructed genetic map comprising eight LGs spanned a total map length of 949.42 cM with an average inter-marker distance of 1.138 cM (Supplementary Table S5). The map length covered by each LG varied from 71.57 cM (62 markers) in LG8 to 157.80 cM (162 markers) in LG4. The most saturated LG was LG4 (average inter-marker distance of 0.974 cM), whereas LG1 was least saturated (1.647 cM) (Supplementary Table S5). Assuming ∼740 Mb genome size of chickpea, the 834 marker-based genetic linkage map had mean marker density of one marker per 887.3 kb. Interestingly, 76 major hot-spot regions were identified on eight LGs of genetic map in which more than two markers were mapped and clustered within 1 cM genetic distance.Figure 1.


An integrated genomic approach for rapid delineation of candidate genes regulating agro-morphological traits in chickpea.

Saxena MS, Bajaj D, Das S, Kujur A, Kumar V, Singh M, Bansal KC, Tyagi AK, Parida SK - DNA Res. (2014)

Nineteen genomic regions harbouring 27 significant QTLs (15.6–39.8% R2) associated with SW, NP, NB and PH were identified and mapped on eight LGs (LOD > 4.0 at P < 0.05) using a 229 RIL mapping population (ICC 4958 × ICC 17160) of chickpea. The genetic distance (cM) and identity of the marker loci integrated on the chromosomes are indicated on the left and right sides of the LGs, respectively. The 15 major and robust QTLs are marked with yellow boxes. The marker pairs flanking the QTLs are coloured with red and blue. Blue, violet, green and brown lines indicate the QTLs regulating SW, NB, NP and PH mapped on eight LGs. The direction of QTLs (additive effects) are designated with empty (ICC 17160-specific alleles) vs. filled (ICC 4958-specific alleles) boxes. *qSW2.1, qSW4.1, qNP8.1 and qNB1.2 correspond to known QTLs from previous studies by Cobos et al.,53,54 Hossain et al.,55 Varshney et al.56 and Gowda et al.57 This figure appears in colour in the online version of DNA Research.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4263302&req=5

DSU031F1: Nineteen genomic regions harbouring 27 significant QTLs (15.6–39.8% R2) associated with SW, NP, NB and PH were identified and mapped on eight LGs (LOD > 4.0 at P < 0.05) using a 229 RIL mapping population (ICC 4958 × ICC 17160) of chickpea. The genetic distance (cM) and identity of the marker loci integrated on the chromosomes are indicated on the left and right sides of the LGs, respectively. The 15 major and robust QTLs are marked with yellow boxes. The marker pairs flanking the QTLs are coloured with red and blue. Blue, violet, green and brown lines indicate the QTLs regulating SW, NB, NP and PH mapped on eight LGs. The direction of QTLs (additive effects) are designated with empty (ICC 17160-specific alleles) vs. filled (ICC 4958-specific alleles) boxes. *qSW2.1, qSW4.1, qNP8.1 and qNB1.2 correspond to known QTLs from previous studies by Cobos et al.,53,54 Hossain et al.,55 Varshney et al.56 and Gowda et al.57 This figure appears in colour in the online version of DNA Research.
Mentions: A set of 839 including 470 genic and genomic SSR markers (Supplementary Fig. S2) and 369 TF gene-derived SNP markers (Supplementary Fig. S3) showing polymorphism between parental accessions were genotyped in 229 individuals of a RIL mapping population (ICC 4958 × ICC 17160) to construct an inter-specific genetic linkage map in chickpea. The linkage analysis using the markers showing significant Mendelian segregation ratio (1:1) mapped 834 markers (including 468 SSR and 366 SNP markers) on eight LGs (LG1–LG8) of chickpea (Fig. 1) according to their physical positions (bp) on respective chromosomes (Supplementary Fig. S1). The constructed genetic map comprising eight LGs spanned a total map length of 949.42 cM with an average inter-marker distance of 1.138 cM (Supplementary Table S5). The map length covered by each LG varied from 71.57 cM (62 markers) in LG8 to 157.80 cM (162 markers) in LG4. The most saturated LG was LG4 (average inter-marker distance of 0.974 cM), whereas LG1 was least saturated (1.647 cM) (Supplementary Table S5). Assuming ∼740 Mb genome size of chickpea, the 834 marker-based genetic linkage map had mean marker density of one marker per 887.3 kb. Interestingly, 76 major hot-spot regions were identified on eight LGs of genetic map in which more than two markers were mapped and clustered within 1 cM genetic distance.Figure 1.

Bottom Line: Most of these QTLs showed positive additive gene effects with effective allelic contribution from ICC 4958, particularly for increasing seed weight (SW) and pod and branch number.This enabled to delineate a strong SW-regulating ABI3VP1 transcription factor (TF) gene at trait-specific QTL interval and consequently identified favourable natural allelic variants and superior high seed weight-specific haplotypes in the upstream regulatory region of this gene showing increased transcript expression during seed development.The genes (TFs) harbouring diverse trait-regulating QTLs, once validated and fine-mapped by our developed rapid integrated genomic approach and through gene/QTL map-based cloning, can be utilized as potential candidates for marker-assisted genetic enhancement of chickpea.

View Article: PubMed Central - PubMed

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

Show MeSH
Related in: MedlinePlus