QTLs mapping linked with cotton leaf curl disease resistance and morphological traits in cotton using microsatellite markers

Abstract

Most essential fiber crop in the world is cotton which is also important economic crop for cotton producing countries. Improvement in the human live standards continuously increasing demand of this fiber due to its possessions feature including natural, thermal insulation, humidity absorption, free of electrostatic and air permeability. In order to increase productivity of cotton through breeding programs continuously focused by the researchers by developing more productive cotton cultivars having resistant against biotech and a biotech stresses. With the improvement in biotechnology molecular breeding has become a very helpful tool for genetic improvement of cotton using marker assistant selection (MAS). In Pakistan, India, Africa and some parts of China Cotton leaf curl disease (CLCuD) is a serious danger to cotton productivity from a long time. The ultimate objective of this study was to identify the genetic inheritance and genomic position associated with CLCuD resistance and other agronomical traits contributing for cotton yield using microsatellites markers. Germplasm screening for CLCuD severity were performed on 100 Gossypium hirsutum (G. hirsutum) genotypes to select most tolerant and susceptible lines. Two genotypes named MNH-886, AGC-555 were selected as highly tolerant, while genotype S-12 was selected as highly susceptible genotype, two F2:3 segregating mapping populations were developed from these selected parents. About 1350 simple sequence repeat (SSRs) markers available at Cotton molecular breeding Laboratory University of Georgia, Tifton, U.S.A were used to screen out polymorphism between the diverse parents. About 111 markers were polymorphic between the S-12 and MNH-886 in Pop 1 and 77 markers were polymorphic between S-12 and AGC-555 in Pop 2. A linkage map of 111 loci was established in segregating mapping Pop 1 with 26 linkage groups covering 767.2 cm of genetic map while a linkage map of 107 loci was established in segregating mapping Pop 2with 18 linkage groups covering 219.4 cm of genetic map. In the first study (Chapter No 5) 15 QTLs associated with CLCuD resistance with LOD score 3.20 to 6.21 supplying PV % ranging from 8.93 to 16.66 were identified in Pop 1. In F2 populations QTL QTLqCLCuD1-11-m2 were detected with flanked markers CIR216 and JESPR158 on chromosome number 11 with LOD score of 3.83. QTL QTLqCLCuD1- 21-m2 was identified in the interval flanked by two SSR markers JESPR158 and JESPR135 with LOD value of 3.67 having 8.68 PV% for mean CLCuD severity at its homologous chromosome number 21. Another identification of QTL qCLCuD1-11-120d2 was between flanked markers DPL209 and BNL4094 at chromosome number 11 with CLCuD severity reading after 120 days having LOD score of 3.13 with 8.0 PV%. QTLs identification in F3 populationprogress to verify this region linked to CLCuD with detection of a major QTL qCLCuD1-11-m3 between flanked markers CIR316 and BNL4094 with higher LOD score of 6.21 in mean values with 16.66 PV%. In F3 population three other QTLs qCLCuD1-11-60d3, qCLCuD1-11-90d3, qCLCuD1-11-120d3 were identified on the chromosome number. 11 with between flanked markers; DPL209 and BNL4094 at 60 days CLCuD severity reading, CIR316 and BNL4094 at 90 days CLCuD severity reading and NAU2309 and BNL4094 at 120 days CLCuD severity reading having LOD score of 5.77, 5.04 and 5.40 with 14.94, 13.46 and 15.33 PV% respectively. Above results could be helpful for recognition of genomic region involved with CLCuD resistance, by fine mapping of QTLs identified can be helpful for the selection of resistance sources from germplasm through MAS. In the second study (Chapter No 6) 8 important QTLs associated with CLCuD resistance with LOD score 3.94 to 7.63 supplying PV % ranging from 10.78 to 20.59 were identified at chromosome number 11 in Pop 2.QTL mapping analysis using1350 SSRs markers recognized (JESPR158 and NAU5418) in F2 and (NAU5418, JESPR158 and NAU3377) in F3 linked with CLCuD resistance at chromosome number 11based on different reading data. In F3 population QTL identification at 60 days disease severity reading had maximum LOD score of 8.55 with JESPR158 and NAU3377 which supply about 22.18 PV%. Both the QTLs in F2 and F3 population distinguished at 60 Days reading (qCLCuD-11-60d2, qCLCuD-11-60d3) along with flanking markers NAU5418, JESPR158 and NAU337 with LOD value of 7.63 and 8.55 respectively, which together give 42.77 PV%. Similarly in populations F2 and F3 mean reading values recognized 2 QTLs qCLCuD-11-m2, qCLCuD- 11-m3 with NAU5418, JEPR158 and NAU3377 SSR markers with LOD score of 6.28 and 5.28 respectively, which together supply 28.73 PV%. QTLs distinguished during this study could be helpful to find out resistance sources of CLCuD with screening of these identified SSR markers. In the third study (Chapter No 7) 9 QTLs significantly associated with different morphological traits including, plant height, number of sympodial branches per plant, leaf width, number of bolls per plant, boll weight, seed cotton yield and sympodial branches per plant with LOD score 2.55 to 3.77 supplying PV % ranging from 7.04to 13.34 were identified in Pop 1. SimilarlyIn Pop 2, two QTLs linked with morphological and yield related traits including number of monopodial branches per plant (MPP) and bolls per plant (BPP) were detected in F2 population at chromosome number 26 and 8 with LOD score of 2.52 and 3.74 contributing 9.80 and 12.15 PV % respectively. In F3 population 5 QTLs linked with morphological traits including number of sympodial branches per plant (SPP), plant height (PH), seed index (SI) and leaf width (LW) were detected at chromosome number 11 and 9 with LOD score 3.52 to 4.28 supplying PV % ranging from 9.25 to 14.49. On the basis of present study screening of more SSR markers especially in the identified regions, fine mapping and QTLs validation could be possible to recognize genomic regions responsible for CLCuD resistance. Identification of these QTLs by SSR markers linked with CLCuD and other morphological key traits could be helpful for plant breeders to select their desired genotype containing a specific trait from the accession of large germplasm.