Screening for Waterlogging Stress Tolerance, Molecular Characterization Using Ssr Markers & In Silico Development of Est -ssr Primers in Pigeonpea (Cajanus Cajan)

Abstract

Pigoonpea ban important puiS<: crop of India and main source of protem for m~t of the population. Waterlogging i~ SC\ ere problem and reduced production that IS "'h)' "'e ha\e done primary screening with 128 accc:55ioru; of pisconpea to identil} diver.e waterlogging stress tolerance genotypes. Only 38 accessions survived nnd funher evaluated for ten different morphological characters vi7 .• chiQI'Oph) II content, plant height. days to 50"/o Oowering. days to plant maturity, pnmary branch, da~ to no .... c:r 1n.tmtion, days to pod mitiallon etc ha~e used Mnhnlnnobis 0 1 statistics. Sigmticnnt differences were observed among the genotype>. Based on the genetic di~tance nil the 38 genotyp.:~ were grouped under !'.even different clu~tc:rs The maximum d1stance Wll> ob<;erved between dusters Vll and V. Generic di\ersity by SSR m4rlo.ers ""1LS po:rfomu:d in a set of38 pigeonpe4t:enotypes. Ty,ent}·two polymOfllhic sequence repeat marl..= \\etc screened across these genOI)pn, and only nine of them amplifiCd a total of I J alleles "ith an a\ erage I A allcl5 per locus. PIC \alue• ranged from 0 to 0.86 "ith an 1\c:ragc: of 0.21 indicating a considerable cfficic:nC) of market> for studying the polymorphism level in pigconpen gennplnsm. Cluster onaly~is, done by UPOMA, grouped the 38 pigconpea genotypes mto two main clusters. Cluster I was • represented by six genotypes and clu~ter II wns represented by totol number of thiny rwo genotypes The present study helps in finding out IC<ISibility of screened SSR mnrkc:rs to be used m genetic diversit) analysis and the1r potentiala.,..oc.ation With specific c:haractm. EST derived SSR marl.ers represent the transcriptome, thus, directl) linked to functional genes. The present report describe:~ the in lilico mining of the microsatellites (SSRs) uo;ing Cajanw cajon EST' from six different cDr-A libraries available m the publi.: domam of 1\CBL A total of :!4176 F..ST> \\ere do"nloaded. From these EST'. 1547 contigs \\ere <>bt3ined \\ith the help ofCAP3 online soli\> arc and 193 SSR:i \\ert generated by SSRIT tool. From these SSR-ESTs sequences 83 SSRs primer pa1r y,cre designed by PrimerJ online sofh•11re These EST-SSR:i can be u~ as potential microsatellitc nwkcrs for di•ersil} analy~is and marter assisted breeding.