Advertisement
Towards fine mapping of drought tolerance related QTL region in chickpea (Cicer arietinum L.)
Upcoming SlideShare
Poster64: QTL mapping of resitance to Thips palmi Karny in common bean (Phase...Poster64: QTL mapping of resitance to Thips palmi Karny in common bean (Phase...
Loading in ... 3
1 of 1
Advertisement

More Related Content

Similar to Towards fine mapping of drought tolerance related QTL region in chickpea (Cicer arietinum L.)(20)

More from ICRISAT(20)

Advertisement

Towards fine mapping of drought tolerance related QTL region in chickpea (Cicer arietinum L.)

  1. Terminal drought is one of major constraints that lead to considerable yield losses (~50%) in chickpea. By using linkage mapping approach on ICC 4958 × ICC 1882 population, a genomic region (~35cM) harbouring several QTLs for drought tolerance related traits was identified on linkage group 4 (LG04). This region contained only four markers (TAA170, ICCM0249, STMS11 and GA24). In order to increase marker density in this region, two approaches were adopted: (a) targeted mapping from the corresponding region from published maps in chickpea, and (b) Medicago-Cicer synteny approach. In the former approach, a set of 43 SSR markers were chosen from the corresponding region on the published genetic maps and genotyping data were generated for 19 polymorphic markers. In the later approach, syntenic regions on Medicago chromosome 1 were identified by aligning the tentative orthologous (TOG) markers present in the corresponding genomic region on the interspecific map (ICC 4958 × PI 489777). In summary, a set of 591 primer pairs were designed from this syntenic region, of which 144 primers produced successful amplification in the intraspecific mapping population. A total of 75 SNPs were identified between the parental genotypes through allele specific sequencing. Only 32 SNPs were found CAPS convertible and 3 markers were polymorphic between the parental lines. By combining these two approaches, three SSR marker loci and three DArT loci were mapped in the QTL region for the intraspecific mapping population. At present, efforts are underway to saturate this region by using RAD-sequencing approach on the mapping population. Abstract Towards fine mapping of drought tolerance related QTL region in chickpea (Cicer arietinum L.) Jaganathan D1, Thudi M1, Tuteja R2, Gaur PM1, Varshney RK1,3* 1International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India 2National University of Ireland (NUI), Galway, Ireland 3Generation Challenge Programme (GCP), c/o CIMMYT, Mexico DF, Mexico *Corresponding author : r.k.varshney@cgiar.org cpPb-49086723.5 Ca17738424.8 cpPb-32675826.2 STMS1127.0 TA4L-TA191R_291-28427.2 GA2427.4 GAA4727.7 LN5A28.2 P32_PisPR32_128.6 DSI29.3 CALTL29.5 M853_Mtmt_GEN_00853_01_129.6 cpPb-32544130.4 cpPb-32653730.5 CGMM00230.9 cpPb-32657631.9 ICCM029332.2 REP32.5 cpPb-323648 cpPb-68238240.2 cpPb-32793640.9 RL342.8 CGMM03643.3 LG9943.7 cpPb-48874344.3 cpPb-49059344.4 cpPb-172867 cpPb-679062 cpPb-678437 45.1 TA4L-TA199R-3_30046.1 cpPb-32796047.2 cpPb-32600847.5 ICCM000448.7 ICCM000348.8 ICCeM01349.5 GA249.9 ICCM002450.5 Ca1286316974739951.4 TA13052.5 TA3L-TS62R52.8 ICCM006353.5 ICCM024953.6 cpPb-32373853.9 TAA17054.6 CaM023256.7 cpPb-67829657.9 Thudi et al. 2011 QTL hot-spot on LG04 (ICC 4958 × ICC 1882) 1 2 Radhika et al. 2007 Millan et al. 2010 TA2x TS54 TA146 TR35 TA72 UBC721 RGA8y TR20s H1A12 H4G11 UBC149z H4E09 NCPGR74 RGA8x TA186 SSR6x SSR6y TS46 H1A10y GA11 UBC335x NCPGR58 H1G22 TS72 UBC844 UBC859y H3A07 UBC335y NCPGR98 UBC840 NCPGR27 TAA170 UBC886 UBC43x UBC54 NCPGR93 UBC43y UBC681 NCPGR45 NCPGR21 TR43 UBC149x GA24 UBC809y H3A04 UBC71y NCPGR34 60 65 70 75 80 85 90 95 100 105 110 115 120 125 FCB TA136 TA61 TR11 UBC181a PsGEN3 ISSR8843 PR10_unten UBC733b OPX131408 TA4LTA191R291-284 OPAC12403 UBC402 OPA14-1 OPAC12450 GAA47 LN5A STMS11 GA24 PsPR32 UBC884b TA4L-TA199R-3_300 OPAF161025 MmGEN12 OPM02950 EAAMCTT08 TA3L-TS62R TA130 R11899 GA2 OPQ05293 CS44a OPAF16985 Enp2 EAAMCTA13 ISSR8401 UBC721b UBC836b TA186 EAAMCTT01 ECAMCAC03 TS54 TA2 TA146 0 5 10 15 20 25 30 35 40 45 50 55 Targeted marker development  A total of 43 markers that are flanking ICCM0249, TAA170, STMS11 and GA24 were selected from published genetic maps (Thudi et al. 2011; Millan et al. 2010; Nayak et al. 2010; Kottapalli et al. 2009; Radhika et al. 2007) Synteny based marker development Additional markers in QTL region Summary Acknowledgements TA640.0 CaM061519.3 CaM084520.5 CaM085620.7 CaM065823.6 NCPGR17125.8 CaM082126.6 NCPGR14127.8 CaM198830.9 ICCM0199c34.9 H1H1336.3 CaM210338.5 ICCM0197a38.6 H1N1240.2 CaM115841.7 H1D2442.3 ICCM006543.2 ICCM016043.7 H2I0145.2 CaM183546.0 CaM130646.1 CaM0410 TR847.1 CaM1903 TAA5849.0 TA7250.0 TA13550.4 STMS2850.9 ICCeM001851.2 ICCeM005951.5 TA7851.7 ICCeM005852.0 CaM132853.8 CISR11754.6 cpPb-682025 cpPb-49040654.8 ICCeM005055.2 TA13255.7 cpPb-32292155.9 cpPb-67686856.5 STMS956.8 CaM168457.4 NCPGR3058.0 CaM043458.5 STMS1458.6 CaM115758.9 NCPGR3159.4 CaM092359.8 TS1959.9 CaM064560.3 CaM107760.5 CaM2093 CaM1026 CaM092460.9 CaM011361.1 CaM050761.3 NCPGR2762.2 NCPGR762.5 ICCM006962.6 ICCM006862.7 ICCM025063.0 H1B1763.3 NCPGR24563.8 TR2064.5 NCPGR23165.2 H1A1965.7 H4G1165.9 TA1866.7 NCPGR23667.1 CaM090668.2 H1A1272.0 CaM204973.6 TA4676.9 ICCM024978.8 ICCM025783.8 NCPGR12788.1 TAA17094.2 NCPGR2197.3 cpPb-680552102.8 cpPb-490776 cpPb-678284105.4 GA24108.2 STMS11111.2 CaM0446123.4 Tp684964131.7 NCPGR91148.3  A total of six new markers (three SSR markers and three DArT loci) are mapped in the QTL region Markers highlighted in red are additional markers added in the present study and markers in blue are previously reported markers in the QTL region  A total of 19 polymorphic SSR markers, 3 CAPS, 5 EST-SSR markers and 14 previously unmapped DArT loci were used for integration into genetic map  Targeted and synteny based approaches resulted in addition of six new markers (ICCM0257, NCPGR21, NCPGR127, cpPb-680552, cpPb-490776 and cpPb-678284) in the QTL region  SNPs identified from RAD sequencing will be used for increasing the markers density Financial support from Generation Challenge program (GCP), Australia-India Strategic Research Fund (AISRF) and technical assistance from Neetu Singh, Katta Sushmita, Preethi Dauthal are greatly appreciated Alignined against Medicago Priority region 1 Priority region 2 TOG markers with in 5cM upstram and down stream of QTL markers on Thudi et al. 2011 is Priority region 1 and within 10cM is Priority region 2 RAD sequencing for SNP marker development Restriction site associated DNA (RAD) sequencing is one of the quick approaches for discovery of large scale SNP markers The parental genotypes of mapping population (ICC 4958 and ICC 1882), 208 recombinant inbred lines (RILs), JG 11 and 33 near isogenic lines (NILs) were used for RAD sequencing On an average 654 SNPs were identified among RILs and 191 SNPs were identified among NILs Multiple sequence alignment of sequences generated through allele-specific sequencing for identification of SNPs among ICC 4958, ICC 1882, ICC 283, ICC 8261 and PI 489777 LG04 of chickpea is syntenic to chromosome 1 of Medicago truncatula (Nayak et al. 2010; Milan et al. 2010) QTL hot-spot on LG04 (ICC 4958 × ICC 1882) 80 Tentative orthologous gene (TOG) based markers selected (Hiremath et al. 2012) 702 genes identified from Mt1 (19.5 Mb to 23.5 Mb) 591 CISR primer pairs designed 341 CISR markers Sequenced 75 SNPs identified and 32 converted to CAPS 3 CAPS polymorphic 0
Advertisement