Development of Genomic Resources in Okra Abelmoschus esculentus L Moench Using Next Generation Sequencing

Abstract

Okra (Abelmoschus esculentus L. Moench) an annual, often cross-pollinated crop newlinebelonging to the family Malvaceae is an important vegetable crop of tropics and subtropics of newlinethe world. At the genome level, okra is regarded as a minor crop, and until very recently, newlinelittle emphasis was given to genetic and genomic studies. The present study reports the first newlinein-depth analysis of the combined total RNA transcriptome of okra using next generation newlinesequencing. Efforts have been made to identify and standardize genic SSRs and developing a newlinelinkage map. newlineIts production experiences many abiotic and biotic stresses. Several studies examined newlineon these stresses only at physiological and biochemical level. However, until date there is no newlineinformation in okra with respect to long non-coding RNAs (lncRNA) and few transcription newlinefactors for abiotic stress on the whole genome scale. Using comprehensive pooled newlinetranscriptome data, this study identified 57,675 lncRNAs and classified into three groups and newlinevalidated them. We also documented 112,597 unigenes and 1,281 TFs. This study presents newlinethe first comprehensive transcriptome data, using RNA from different parts of okra such as newlineroot, stem, leaf, bud, flower, different stages of developing pod and from twenty days old newlineplantlets of heat, drought and salt stress. A total of 10,492 SSRs were identified in this study. newlineThe lack of appropriate genetic markers, linkage maps, and reference genomes has newlineinhibited application of advanced breeding methods in okra. A total of 358 F2 mapping newlinepopulations were developed and screened for YVMV tolerance. The ratio for YVMV newlinetolerance indicated 3:1 segregation of recessive resistance. From GBS data analysis a total of newline4599 single nucleotide polymorphisms (SNPs) were identified and distributed across 65 newlinechromosomes. These SNPs were distributed among chromosome from LG-1 to LG-65. The newlinegenetic distance of linkage group ranged from 8.683 to 17961.301 cM. newlineA comparative transcriptome profiling, and gene expression analysis in an effort to newlineidentify gene networks that are associated with yellow vein mosaic virus (YVMV) resistance newlinewas carried out. The results of the RNAseq data revealed that the virus infection of resistant newlineplants resulted in an up regulation of the genes such as Nudix hydrolase, SAG 21, Peroxidase, newlineRING-H2 finger protein, GRXC-6, NBS-LRR and bHLH-TFs. Although YVMV expression newlinewas enhanced with NAC and MAPKKK.3 genes in susceptible plants. Higher constitutive or newlineinduced levels of biochemical compounds, such as phenols, flavonoids, antioxidant enzymes newline newlineDevelopment of Genomic Resources in Okra Abelmoschus esculentus (L.) Moench Using Next Generation newlineSequencing newline newlineM. Gayathri newlineand profiling of phenols, flavonoids and hormones related to plant resistance were also newlineobserved in the resistant inoculated plants. newlineThe identified lncRNAs and TFs in this study will aid in understading the structure of newlineokra genome and the molecular changes during plant growth, development and its response to newlinebiotic and abiotic stresses. The genic SSR markers developed will help in germplasm newlinecharacterization mapping, genetic diversity studies, marker assisted breeding and also in gene newlinediscovery. The linkage map construction in okra is the first report in this crop using GBS. newlineFurther research on the QTLs and MAS for the YMD resistant trait will be aided by the data newlineproduced by this work. Additionally, this can be used to create YMD resistant genotypes and newlineanalyse the YMD resistance in okra at the molecular level. The genes with positive and newlinenegative regulators of virus resistance were observed in the present study. These findings will newlinefacilitate breeding and genetic engineering efforts to incorporate novel sources of YVMV newlineresistance in okra. newline