title: Plant exomics: concepts, applications and methodologies in crop improvement.
abstract: Molecular breeding has a crucial role in improvement of crops. Conventional breeding techniques have failed to ameliorate food production. Next generation sequencing has established new concepts of molecular breeding. Exome sequencing has proven to be a significant tool for assessing natural evolution in plants, studying host pathogen interactions and betterment of crop production as exons assist in interpretation of allelic variation with respect to their phenotype. This review covers the platforms for exome sequencing, next generation sequencing technologies that have revolutionized exome sequencing and led toward development of third generation sequencing. Also discussed in this review are the uses of these sequencing technologies to improve wheat, rice and cotton yield and how these technologies are used in exploring the biodiversity of crops, providing better understanding of plant-host pathogen interaction and assessing the process of natural evolution in crops and it also covers how exome sequencing identifies the gene pool involved in symbiotic and other co-existential systems. Furthermore, we conclude how integration of other methodologies including whole genome sequencing, proteomics, transcriptomics and metabolomics with plant exomics covers the areas which are left untouched with exomics alone and in the end how these integration will transform the future of crops.
authors.affiliation: a Atta ur Rahman School of Applied Biosciences ; National University of Sciences and Technology ; Islamabad , Pakistan.
authors.forename: Uzair
authors.initials: U
authors.lastname: Hashmi
authors.forename: Samia
authors.initials: S
authors.lastname: Shafqat
authors.forename: Faria
authors.initials: F
authors.lastname: Khan
authors.forename: Misbah
authors.initials: M
authors.lastname: Majid
authors.forename: Harris
authors.initials: H
authors.lastname: Hussain
authors.forename: Alvina Gul
authors.initials: AG
authors.lastname: Kazi
authors.forename: Riffat
authors.initials: R
authors.lastname: John
authors.forename: Parvaiz
authors.initials: P
authors.lastname: Ahmad
mesh_terms: D018556:Crops, Agricultural / Q000235:genetics*; D059472:Exome / Q000502:physiology*; D005091:Exons / Q000235:genetics*; D018506:Gene Expression Regulation, Plant / Q000502:physiology*; D014644:Genetic Variation; D018745:Genome, Plant; D010940:Plant Proteins / Q000235:genetics / Q000378:metabolism*; D017422:Sequence Analysis, DNA / Q000639:trends
chemical_list: D010940:Plant Proteins
keywords: BAC, bacterial artificial chromosome; BGR, bacterial grain rot; CBOL, consortium for 860 the barcode of life; ETI, effector-triggered immunity; HPRT, hypoxanthineguanine phosphoribosyl transferase; MMs, molecular markers; NGS, next generation sequencing; NITSR, nuclear internal transcribed spacer region; OPC, open promoter complex; QTL, quantitative trait locus; SMRT, single molecule real time; SNPs, single nucleotide poly-morphisms; SOLiD, sequencing by oligonucleotide ligation and detection; WES, whole exome sequencing; WGS, whole genome sequencing; WGS, whole genome shotgun; biodiversity; crop improvement; dNMPs, deoxyribosenucleoside monophosphates; exome sequencing; plant biotechnology; plant-host pathogen interactions