Limits...
Two key genomic regions harbour QTLs for salinity tolerance in ICCV 2 × JG 11 derived chickpea (Cicer arietinum L.) recombinant inbred lines.

Pushpavalli R, Krishnamurthy L, Thudi M, Gaur PM, Rao MV, Siddique KH, Colmer TD, Turner NC, Varshney RK, Vadez V - BMC Plant Biol. (2015)

Bottom Line: Salinity significantly (P < 0.05) affected almost all traits across years and yield reduction was in large part related to a reduction in seed number but also a reduction in above ground biomass.The QTL analysis revealed two key genomic regions on CaLG05 (28.6 cM) and on CaLG07 (19.4 cM), that harboured QTLs for six and five different salinity tolerance associated traits, respectively, and imparting either higher plant vigour (on CaLG05) or higher reproductive success (on CaLG07).Based on the gene ontology annotation, forty eight putative candidate genes responsive to salinity stress were found on CaLG05 (31 genes) and CaLG07 (17 genes) in a distance of 11.1 Mb and 8.2 Mb on chickpea reference genome.

View Article: PubMed Central - PubMed

Affiliation: International Crops Research Institute for the Semi-Arid Tropics, Patancheru 502 234, Telangana State, India. pushpavalli11@gmail.com.

ABSTRACT

Background: Although chickpea (Cicer arietinum L.), an important food legume crop, is sensitive to salinity, considerable variation for salinity tolerance exists in the germplasm. To improve any existing cultivar, it is important to understand the genetic and physiological mechanisms underlying this tolerance.

Results: In the present study, 188 recombinant inbred lines (RILs) derived from the cross ICCV 2 × JG 11 were used to assess yield and related traits in a soil with 0 mM NaCl (control) and 80 mM NaCl (salinity) over two consecutive years. Salinity significantly (P < 0.05) affected almost all traits across years and yield reduction was in large part related to a reduction in seed number but also a reduction in above ground biomass. A genetic map was constructed using 56 polymorphic markers (28 simple sequence repeats; SSRs and 28 single nucleotide polymorphisms; SNPs). The QTL analysis revealed two key genomic regions on CaLG05 (28.6 cM) and on CaLG07 (19.4 cM), that harboured QTLs for six and five different salinity tolerance associated traits, respectively, and imparting either higher plant vigour (on CaLG05) or higher reproductive success (on CaLG07). Two major QTLs for yield in the salinity treatment (explaining 12 and 17% of the phenotypic variation) were identified within the two key genomic regions. Comparison with already published chickpea genetic maps showed that these regions conferred salinity tolerance across two other populations and the markers can be deployed for enhancing salinity tolerance in chickpea. Based on the gene ontology annotation, forty eight putative candidate genes responsive to salinity stress were found on CaLG05 (31 genes) and CaLG07 (17 genes) in a distance of 11.1 Mb and 8.2 Mb on chickpea reference genome. Most of the genes were known to be involved in achieving osmoregulation under stress conditions.

Conclusion: Identification of putative candidate genes further strengthens the idea of using CaLG05 and CaLG07 genomic regions for marker assisted breeding (MAB). Further fine mapping of these key genomic regions may lead to novel gene identification for salinity stress tolerance in chickpea.

No MeSH data available.


QTLs for five different traits were identified across years and treatments on CaLG07. A. Genomic region on CaLG07 that harboured the 9 QTLs for traits that conferred salinity tolerance in ICCV 2 × JG 11 population were identified using QTL cartographer. B. CaLG07 in ICCV 2 × JG 11 population corresponded to LG 7 in Thudi et al. 2011 and LG5 in Vadez et al. 2012.
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Fig2: QTLs for five different traits were identified across years and treatments on CaLG07. A. Genomic region on CaLG07 that harboured the 9 QTLs for traits that conferred salinity tolerance in ICCV 2 × JG 11 population were identified using QTL cartographer. B. CaLG07 in ICCV 2 × JG 11 population corresponded to LG 7 in Thudi et al. 2011 and LG5 in Vadez et al. 2012.

Mentions: The genomic region of CaLG05 flanked by markers CaM0463 and ICCM272 contained 17 major QTLs for seven different traits (DF, DM, ADM, stem + leaf weight, 100-seed weight, HI and yield) across treatments (Figure 1). Furthermore, one major QTL for DF, DM, ADM, HI, 100-seed weight and yield in the salinity treatment was found in this region. Another genomic region, on CaLG07, harboured seven QTLs, out of which 5 QTLs were identified in the salinity treatment for five different traits (DF, DM, seed number, pod number and yield), but none of these QTLs were stable (Figure 2). A genomic region on CaLG08 harboured eight QTLs (6 in the control treatment and 2 in the salinity treatment) for three traits, DF, DM and HI. Out of these three genomic regions, the genomic regions on CaLG05 and CaLG07 were of greatest interest as they hold QTLs for traits that were significantly related to yield under salinity (Additional file 11: Figure S1).Figure 1


Two key genomic regions harbour QTLs for salinity tolerance in ICCV 2 × JG 11 derived chickpea (Cicer arietinum L.) recombinant inbred lines.

Pushpavalli R, Krishnamurthy L, Thudi M, Gaur PM, Rao MV, Siddique KH, Colmer TD, Turner NC, Varshney RK, Vadez V - BMC Plant Biol. (2015)

QTLs for five different traits were identified across years and treatments on CaLG07. A. Genomic region on CaLG07 that harboured the 9 QTLs for traits that conferred salinity tolerance in ICCV 2 × JG 11 population were identified using QTL cartographer. B. CaLG07 in ICCV 2 × JG 11 population corresponded to LG 7 in Thudi et al. 2011 and LG5 in Vadez et al. 2012.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4440540&req=5

Fig2: QTLs for five different traits were identified across years and treatments on CaLG07. A. Genomic region on CaLG07 that harboured the 9 QTLs for traits that conferred salinity tolerance in ICCV 2 × JG 11 population were identified using QTL cartographer. B. CaLG07 in ICCV 2 × JG 11 population corresponded to LG 7 in Thudi et al. 2011 and LG5 in Vadez et al. 2012.
Mentions: The genomic region of CaLG05 flanked by markers CaM0463 and ICCM272 contained 17 major QTLs for seven different traits (DF, DM, ADM, stem + leaf weight, 100-seed weight, HI and yield) across treatments (Figure 1). Furthermore, one major QTL for DF, DM, ADM, HI, 100-seed weight and yield in the salinity treatment was found in this region. Another genomic region, on CaLG07, harboured seven QTLs, out of which 5 QTLs were identified in the salinity treatment for five different traits (DF, DM, seed number, pod number and yield), but none of these QTLs were stable (Figure 2). A genomic region on CaLG08 harboured eight QTLs (6 in the control treatment and 2 in the salinity treatment) for three traits, DF, DM and HI. Out of these three genomic regions, the genomic regions on CaLG05 and CaLG07 were of greatest interest as they hold QTLs for traits that were significantly related to yield under salinity (Additional file 11: Figure S1).Figure 1

Bottom Line: Salinity significantly (P < 0.05) affected almost all traits across years and yield reduction was in large part related to a reduction in seed number but also a reduction in above ground biomass.The QTL analysis revealed two key genomic regions on CaLG05 (28.6 cM) and on CaLG07 (19.4 cM), that harboured QTLs for six and five different salinity tolerance associated traits, respectively, and imparting either higher plant vigour (on CaLG05) or higher reproductive success (on CaLG07).Based on the gene ontology annotation, forty eight putative candidate genes responsive to salinity stress were found on CaLG05 (31 genes) and CaLG07 (17 genes) in a distance of 11.1 Mb and 8.2 Mb on chickpea reference genome.

View Article: PubMed Central - PubMed

Affiliation: International Crops Research Institute for the Semi-Arid Tropics, Patancheru 502 234, Telangana State, India. pushpavalli11@gmail.com.

ABSTRACT

Background: Although chickpea (Cicer arietinum L.), an important food legume crop, is sensitive to salinity, considerable variation for salinity tolerance exists in the germplasm. To improve any existing cultivar, it is important to understand the genetic and physiological mechanisms underlying this tolerance.

Results: In the present study, 188 recombinant inbred lines (RILs) derived from the cross ICCV 2 × JG 11 were used to assess yield and related traits in a soil with 0 mM NaCl (control) and 80 mM NaCl (salinity) over two consecutive years. Salinity significantly (P < 0.05) affected almost all traits across years and yield reduction was in large part related to a reduction in seed number but also a reduction in above ground biomass. A genetic map was constructed using 56 polymorphic markers (28 simple sequence repeats; SSRs and 28 single nucleotide polymorphisms; SNPs). The QTL analysis revealed two key genomic regions on CaLG05 (28.6 cM) and on CaLG07 (19.4 cM), that harboured QTLs for six and five different salinity tolerance associated traits, respectively, and imparting either higher plant vigour (on CaLG05) or higher reproductive success (on CaLG07). Two major QTLs for yield in the salinity treatment (explaining 12 and 17% of the phenotypic variation) were identified within the two key genomic regions. Comparison with already published chickpea genetic maps showed that these regions conferred salinity tolerance across two other populations and the markers can be deployed for enhancing salinity tolerance in chickpea. Based on the gene ontology annotation, forty eight putative candidate genes responsive to salinity stress were found on CaLG05 (31 genes) and CaLG07 (17 genes) in a distance of 11.1 Mb and 8.2 Mb on chickpea reference genome. Most of the genes were known to be involved in achieving osmoregulation under stress conditions.

Conclusion: Identification of putative candidate genes further strengthens the idea of using CaLG05 and CaLG07 genomic regions for marker assisted breeding (MAB). Further fine mapping of these key genomic regions may lead to novel gene identification for salinity stress tolerance in chickpea.

No MeSH data available.