Development and validation of novel fiber relevant dbEST–SSR markers and their utility in revealing genetic diversity in diploid cotton (Gossypium herbaceum and G. arboreum)

Parekh, Mithil J.; Kumar, Sushil; Zala, Harshvardhan N.; Fougat, R. S.; Patel, C. A.; Bosamia, Tejas C.; Kulkarni, Kalyani S.; Parihar, Akarsh

doi:10.1016/j.indcrop.2015.12.061

Cited by 23 publications

(11 citation statements)

References 46 publications

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“…In contrast to research on N 1 and n 2 , few systematic studies have been carried out on the diploid G. arboreum fuzzless mutant DPL972. A comparison of molecular mechanisms between diploids and tetraploids is thus needed (Parekh et al 2016). DPL972 is a near-isogenic line (NIL) of the wild-type DPL971.…”

Section: Introductionmentioning

confidence: 99%

Fine mapping and identification of the fuzzless gene GaFzl in DPL972 (Gossypium arboreum)

Cheng

Zuo

et al. 2019

Theor Appl Genet

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Key message The fuzzless gene GaFzl was fine mapped to a 70-kb region containing a GIR1 gene, Cotton_A_11941, responsible for the fuzzless trait in Gossypium arboreum DPL972. Abstract Cotton fiber is the most important natural textile resource. The fuzzless mutant DPL972 ( Gossypium arboreum ) provides a useful germplasm resource to explore the molecular mechanism underlying fiber and fuzz initiation and development. In our previous research, the fuzzless gene in DPL972 was identified as a single dominant gene and named GaFzl . In the present study, we fine mapped this gene using F 2 and BC 1 populations. By combining traditional map-based cloning and next-generation sequencing, we mapped GaFzl to a 70-kb region containing seven annotated genes. RNA-Sequencing and re-sequencing analysis narrowed these candidates to two differentially expressed genes, Cotton_A_11941 and Cotton_A_11942. Sequence alignment uncovered no variation in coding or promoter regions of Cotton_A_11942 between DPL971 and DPL972, whereas two single-base mutations in the promoter region and a TTG insertion in the coding region were detected in Cotton_A_11941 in DPL972. Cotton_A_11941 encoding a homologous gene of GIR1 (GLABRA2 - interacting repressor) in Arabidopsis thaliana is thus the candidate gene most likely responsible for the fuzzless trait in DPL972. Our findings should lead to a better understanding of cotton fuzz formation, thereby accelerating marker-assisted selection during cotton breeding. Electronic supplementary material The online version of this article (10.1007/s00122-019-03330-3) contains supplementary material, which is available to authorized users.

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Section: Introductionmentioning

confidence: 99%

Fine mapping and identification of the fuzzless gene GaFzl in DPL972 (Gossypium arboreum)

Cheng

Zuo

et al. 2019

Theor Appl Genet

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“…The newly developed SSRs with regard to the transcripts derived from RNA-seq were referred to as YSB EST-SSR. We categorized the SSR motifs into perfect SSRs (repeat motifs that are simple tandem sequences, without any interruptions) and compound SSRs (sequences containing two adjacent distinct SSRs, separated by none to any number of base pairs) ( Parekh et al 2016 ). In our study, we kept this distance as 100 bp and excluded mononucleotide repeats to reduce the sequencing errors in the data ( Kalia et al 2011 ).…”

Section: Resultsmentioning

confidence: 99%

RNA-seq of Rice Yellow Stem BorerScirpophaga incertulasReveals Molecular Insights During Four Larval Developmental Stages

Renuka

Maganti

Padmakumari

et al. 2017

G3 Genes|Genomes|Genetics

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The yellow stem borer (YSB), Scirpophaga incertulas, is a prominent pest in rice cultivation causing serious yield losses. The larval stage is an important stage in YSB, responsible for maximum infestation. However, limited knowledge exists on the biology and mechanisms underlying the growth and differentiation of YSB. To understand and identify the genes involved in YSB development and infestation, so as to design pest control strategies, we performed de novo transcriptome analysis at the first, third, fifth, and seventh larval developmental stages employing Illumina Hi-seq. High-quality reads (HQR) of ∼229 Mb were assembled into 24,775 transcripts with an average size of 1485 bp. Genes associated with various metabolic processes, i.e., detoxification mechanism [CYP450, GSTs, and carboxylesterases (CarEs)], RNA interference (RNAi) machinery (Dcr-1, Dcr-2, Ago-1, Ago-2, Sid-1, Sid-2, Sid-3, and Sid-1-related gene), chemoreception (CSPs, GRs, OBPs, and ORs), and regulators [transcription factors (TFs) and hormones] were differentially regulated during the developmental stages. Identification of stage-specific transcripts made it possible to determine the essential processes of larval development. Comparative transcriptome analysis revealed that YSB has not evolved much with respect to the detoxification mechanism, but showed the presence of distinct RNAi machinery. The presence of strong specific visual recognition coupled with chemosensory mechanisms supports the monophagous nature of YSB. Designed expressed sequenced tags-simple-sequence repeats (EST-SSRs) will facilitate accurate estimation of the genetic diversity of YSB. This is the first report on characterization of the YSB transcriptome and the identification of genes involved in key processes, which will help researchers and industry to devise novel pest control strategies. This study also opens up a new avenue to develop next-generation resistant rice using RNAi or genome editing approaches.

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“…Hence, the identification of stable quantitative trait loci (QTL) for irrigated and water deficit environment could facilitate molecular breeding of cotton genotypes with both improved fiber quality and yield attributes. QTL, genetic diversity and structure analysis, require the availability of abundant DNA markers which are continually being developed for the cotton genome [ 49 ]. In upland cotton, several QTL analyses have focused on lint yield traits [ 50 , 51 ], but less attention have been paid to identify QTLs for fiber quality under drought [ 52 ].…”

Section: Fiber Qualitymentioning

confidence: 99%

Coping with drought: stress and adaptive mechanisms, and management through cultural and molecular alternatives in cotton as vital constituents for plant stress resilience and fitness

et al. 2018

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Increased levels of greenhouse gases in the atmosphere and associated climatic variability is primarily responsible for inducing heat waves, flooding and drought stress. Among these, water scarcity is a major limitation to crop productivity. Water stress can severely reduce crop yield and both the severity and duration of the stress are critical. Water availability is a key driver for sustainable cotton production and its limitations can adversely affect physiological and biochemical processes of plants, leading towards lint yield reduction. Adaptation of crop husbandry techniques suitable for cotton crop requires a sound understanding of environmental factors, influencing cotton lint yield and fiber quality. Various defense mechanisms e.g. maintenance of membrane stability, carbon fixation rate, hormone regulation, generation of antioxidants and induction of stress proteins have been found play a vital role in plant survival under moisture stress. Plant molecular breeding plays a functional role to ascertain superior genes for important traits and can offer breeder ready markers for developing ideotypes. This review highlights drought-induced damage to cotton plants at structural, physiological and molecular levels. It also discusses the opportunities for increasing drought tolerance in cotton either through modern gene editing technology like clustered regularly interspaced short palindromic repeat (CRISPR/Cas9), zinc finger nuclease, molecular breeding as well as through crop management, such as use of appropriate fertilization, growth regulator application and soil amendments.

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Development and validation of novel fiber relevant dbEST–SSR markers and their utility in revealing genetic diversity in diploid cotton (Gossypium herbaceum and G. arboreum)

Cited by 23 publications

References 46 publications

Fine mapping and identification of the fuzzless gene GaFzl in DPL972 (Gossypium arboreum)

Fine mapping and identification of the fuzzless gene GaFzl in DPL972 (Gossypium arboreum)

RNA-seq of Rice Yellow Stem BorerScirpophaga incertulasReveals Molecular Insights During Four Larval Developmental Stages

Coping with drought: stress and adaptive mechanisms, and management through cultural and molecular alternatives in cotton as vital constituents for plant stress resilience and fitness

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