IN SILICO MINING OF SSRs FOR MAPPING OF GYNOECY IN BITTER GOURD (Momordica charantia L.)

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dc.contributor.advisorJ. S. ARAVINDA KUMAR
dc.contributor.advisorCHOLIN, SARVAMANGALA S.
dc.contributor.advisorJAWADAGI, RAVEENDRA SANGAPPA.
dc.contributor.advisorD. S. AMBIKA
dc.contributor.authorGUNNAIAH, RAGHAVENDRA.
dc.date.accessioned2023-11-07T11:57:58Z
dc.date.available2023-11-07T11:57:58Z
dc.date.issued2021-04
dc.description.abstractBitter gourd is nutritional and medicinally adorable vegetable. Gynoecy is a condition where flowering node bears only pistillate flowers. Use of gynoecious line as a female parent would provide higher yield and high genetic purity. However, these gynoecious lines are influenced by environment and are governed by recessive genes because of which transferring into elite background is a difficult. So, identification of markers linked gynoecy is of more importance. An investigation on in silico mining of Simple Sequence Repeats (SSRs) from the publicly available restriction associated DNA (RAD) sequence and transcriptome (RNA-seq) of bitter gourd was carried out for mapping of gynoecy in bitter gourd (Momordica charantia L.). RAD sequence assembly of 418832 contigs with mean contig size of 684 bp and N50 contig length of 2383 bp was generated from the quality filtered 19,495,170 paired end RAD-seq reads of gynoecious like K-44 (ERR2214863). Similarly, filtered RNAseq reads of gynoecious (Gy323; SRR947759 and SRR953077) and monoecious line (DRAR-1; SRR950973 and SRR953078) were assembled into 56070 and 51007 unigenes respectively. Assembled unigenes of gynoecious bitter gourd exhibited median contig length of 468 bp, average contig size of 867.55 bp, GC % of 41.19 and N50 contig length of 1553 bp. Monoecious bitter gourd unigenes exhibited median contig length of 440 bp, average contig size of 917 bp, GC% of 41.33 and N50 contig length of 1801 bp. In silico polymorphic SSRs were mined from the assembled RAD-seq genome and transcriptome using CandiSSR bioinformatics pipeline. A total of 3937 gSSRs comprising di, tri, tetra, penta and hexa nucleotide motifs were identified from 1575 RAD-seq assembled contigs. Among them 1591 were polymorphic. A total of 398 eSSRs consisting of di, tri, tetra, penta and hexa nucleotide motifs were predicted across both gynoecious and monoecious bitter gourd lines from assembled transcriptome of bitter gourd gynoecious line (Gy323) and monoecious line (DRAR1). Among them, 222 SSRs were polymorphic. Highest polymorphic SSRs were found on chromosome 08 (36), followed by chromosome 09 (29). Least polymorphic SSRs were identified on chromosome 01 (1), followed by chromosome 02 (11). For validation of the in silico mined polymorphic SSRs, F2 mapping population was developed from the Selfing of F1s derived from the cross between gynoecious line (GY-2) and monoecious line (CO-1). Gynoecy exhibited single recessive inheritance in the F2 mapping population. Thirty-one polymorphic gSSRs and 06 eSSRs were selected based on their ability to resolve on agarose gels. Among the 37 SSR markers tested, none of them exhibited polymorphism between the parents on the 4% agarose gel. On capillary electrophoresis, 03 markers (BG_gSSR253, BG_gSSR3902 and BG_gSSR2363) exhibited polymorphism between gynoecious line and monoecious lines. However, none of the 3 markers exhibited consistent polymorphism among the pooled DNA of 10 each of monoecious and gynoecious F2 lines. In addition to SSR markers, previously reported gynoecy governing chromosomal regions of bitter gourd were sequenced for identification of SNPs between gynoecious and monoecious parents. None of the five SNPs exhibited polymorphism between the monoecious and gynoecious parents. Nonetheless, SSRs developed in this study are novel and may be helpful in mapping gynoecy in other mapping populations.
dc.identifier.otherUHS18PGM1054
dc.identifier.urihttps://krishikosh.egranth.ac.in/handle/1/5810200522
dc.keywordsHorticulture
dc.keywordsBiotechnology
dc.keywordsCrop Improvement
dc.keywordsBitter Gourd
dc.keywordsNutritional
dc.keywordsMedicinal
dc.keywordsGynoecy
dc.keywordsPistillate
dc.keywordsGynoecious
dc.keywordsGenetic
dc.keywordsMarkers
dc.keywordsMining
dc.keywordsTranscriptome
dc.keywordsMonoecious
dc.keywordsUnigenes
dc.keywordsSilico
dc.keywordsPolymorphic
dc.keywordsGenome
dc.keywordsBioinformatics
dc.keywordsTetra
dc.keywordsPenta
dc.keywordsHexa
dc.keywordsNucleotide
dc.keywordsChromosome
dc.keywordsAgarose Gels
dc.keywordsElectrophoresis
dc.keywordsUHS18PGM1054
dc.keywordsT637
dc.language.isoEnglish
dc.pages117p. (Due to pdf. conversion there is a difference in pages of soft copy and hard copy).
dc.publisherUniversity of Horticultural Sciences, Bagalkot. (College of Horticulture, Bagalkot).
dc.subBiotechnology
dc.themeIN SILICO MINING OF SSRs FOR MAPPING OF GYNOECY IN BITTER GOURD (Momordica charantia L.)
dc.these.typeM.Sc
dc.titleIN SILICO MINING OF SSRs FOR MAPPING OF GYNOECY IN BITTER GOURD (Momordica charantia L.)
dc.typeThesis
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