Genetic Dissection Of Boll Size Regulation And Genome Wide Motif Imperfection Analysis In Cotton

1.Map-based cloning qSCW-cl2Enhancing fiber yield is challenging since multiple yield traits determine seed cotton weight?SCW?in cotton.Understanding the precise genetic and biochemical mechanisms underlying the genetic architecture of boll size trait remains a challenge for cotton researchers.To gain insight into genetic basis of yield regulating boll traits in cotton,a small boll bearing mutant,BS41,was identified in an interspecific hybridization derived BIL population which showed hybrid breakdown in boll size regulating traits SCW,lint weight?LW?and seed weight?SW?.Identification of multiple bulk linked markers aided in detection of a stable boll size regulating locus,qSCW-c12,on chrl2.Progeny evaluation confined the qSCW-c12 to 0.89 cM interval between markers AD-A12₀7 and AD-FM₄4 in recombinant derived BC2F4 population.A major effect hybrid break down pleiotropic locus?qSCW-c12?,regulating boll size and yield traits was detected and validated in multiple segregation populations.Substitution fine mapping procedures aided in narrowing the candidate region to a 0,89 cM interval that corresponded to eleven genes contained in 180 Kb region on chromosome GhA12 of Upland cotton.Homology mapping detected a 40-bp insertion-deletion?InDel?site in AD-FM-44 clone sequence,situated +341 downstream of GhBRH1_A12 which showed complete linkage to SCW.Suppressed expression of GhBRH1_A12 in BS41 and Lil transcriptome suggested its putative involvement in regulating fiber development during early boll development events.Despite of featuring suppressed growth,BS41 exhibited active brassinosteroid?BR?homeostasis in developing bolls,thus a disruption in BR signal cascade is anticipated which could be related to lowered GhBRH1_A12 expression in BS41.This study also concluded that GhBH1_A12 is a putative candidate gene determining boll weight,lint weight and seed weight,which are influenced by lint percentage,fiber density and seed number per boll variations through modulation of brassinosteroid biosynthesis and/or signaling pathways in cotton.In conclusion,fine mapping and map-based cloning of a pleiotropic SCW regulating locus,qSCfW-c12,led to identification of GhBRH1_A12,a BR-responsive RING domain containing E3 ligase.2.Functional analysis of GhBRH1_A12 gene family in cottonE3 ligases are key elements in ubiquitin mediated protein degradation system,which have shown potential of regulating plant growth,seed and fruit development in plants.E3 ligases modulate diverse functions by interacting with phytoharmone based biosynthesis and signaling pathways to regulate yield traits in plants.BRH1,a BR-responsive RING-H2 gene encodes a zinc-finger RING domain containing E3 ubiquitin ligase,whose expression could be downregulated by exogenous BR application.Putative BRH1 genes in four cotton genomes were identified through an integrated annotation framework.Two domains were detected in AtBRH1 peptide including;?i?a transmembrane helix?TMH?domain which indicated its putative role in signal transduction,and?ii?a zinc finger containing RING domain which featured with E3 ligase activity.Overall,16,4,7 and 8 putative BRH1genes were identified in G.hirsutum,G.barbadense,G.arboreum and G.raimondii,respectively.The expression pattern of GBRH1 genes in cultivated cotton genome in root,leaf,stem,petal,anther,stigma,ovule,10 DPA,20 DPA fiber and seed tissues were determined using transcriptomic data.Moreover,genetic transformation of GhBRH1_A12,resulted from map-based cloning of a boll size regulating locus,qSCW-c12,was also accomplished.The transgenic plants showing higher expression?BOX2,BOX3 and BOX4?showed more suppressed boll growth resulting in reduced SCW production.3.Evolutionary dynamics of motif imperfection in cotton genomesMechanisms underlying such kind of genetic variations have been broadly investigated in different organisms.However,obscure impact of polidization,an evolutionary process of genome content duplication mostly prevailed to plants,on non-coding DNA is poorly understood.The present study is detailed investigation of motif imperfection pattern in genome assemblies among 13 plant species representing five taxonomic families in plant kingdom.The results explicated evolution and stability of motif-interrupted repeats,its relationship with repeat length and its impact on their genomic prevalence in monocot and dicots.The outcome of this study might be considered a directive to explore comparative evolutionary footprints for simple non-coding genetic elements i.e.,repeats,through the evolution of genus-specific characteristics in cotton genomes.Similarly,short motif repeats exhibited rapid loss through the evolution of Gossypium lineage ensued drastic decrease of 2nt repeats,of which"AT" were dilapidated more rapidly in cotton cultivated tetraploids.However,comprehensive investigations to characterize "AT" motif decay hotspots along with imperfection in four genomes and divulge its impact on modulation of gene regulatory elements is mandatory to further understand fundamental underlying mechanisms,if results of the present study are considered.