scholarly journals Mapping of dwarfing QTL of Ari1327, a semi-dwarf mutant of upland cotton

2022 ◽  
Vol 22 (1) ◽  
Author(s):  
Chenhui Ma ◽  
Abdul Rehman ◽  
Hong Ge Li ◽  
Zi Bo Zhao ◽  
Gaofei Sun ◽  
...  
Keyword(s):  
Plant Height ◽  
Upland Cotton ◽  
Genotyping By Sequencing ◽  
Dwarf Mutant ◽  
Rna Seq ◽  
Indel Markers ◽  
Linkage Information ◽  
Wild Variety ◽  
Key Features ◽  
Genotype A

Abstract Background Upland Cotton (Gossypium hirsutum L.) has few cotton varieties suitable for mechanical harvesting. The plant height of the cultivar is one of the key features that need to modify. Hence, this study was planned to locate the QTL for plant height in a 60Co γ treated upland cotton semi-dwarf mutant Ari1327. Results Interestingly, bulk segregant analysis (BSA) and genotyping by sequencing (GBS) methods exhibited that candidate QTL was co-located in the region of 5.80–9.66 Mb at D01 chromosome in two F2 populations. Using three InDel markers to genotype a population of 1241 individuals confirmed that the offspring’s phenotype is consistent with the genotype. Comparative analysis of RNA-seq between the mutant and wild variety exhibited that Gh_D01G0592 was identified as the source of dwarfness from 200 genes. In addition, it was also revealed that the appropriate use of partial separation markers in QTL mapping can escalate linkage information. Conclusions Overwhelmingly, the results will provide the basis to reveal the function of candidate genes and the utilization of excellent dwarf genetic resources in the future.

scholarly journals Identification of Bna.IAA7.C05 as allelic gene for dwarf mutant generated from tissue culture in oilseed rape

2019 ◽  
Vol 19 (1) ◽  
Author(s):  
Hongtao Cheng ◽  
Fenwei Jin ◽  
Qamar U. Zaman ◽  
Bingli Ding ◽  
Mengyu Hao ◽  
...  
Keyword(s):  
Tissue Culture ◽  
Plant Height ◽  
High Throughput Sequencing ◽  
Agronomic Traits ◽  
Crop Improvement ◽  
Dwarf Mutant ◽  
Sequencing Analysis ◽  
Rna Seq ◽  
Dwarf Phenotype ◽  
Lodging Resistance

Abstract Background Plant height is one of the most important agronomic traits in many crops due to its influence on lodging resistance and yield performance. Although progress has been made in the use of dwarfing genes in crop improvement, identification of new dwarf germplasm is still of significant interest for breeding varieties with increased yield. Results Here we describe a dominant, dwarf mutant G7 of Brassica napus with down-curved leaves derived from tissue culture. To explore the genetic variation responsible for the dwarf phenotype, the mutant was crossed to a conventional line to develop a segregating F2 population. Bulks were formed from plants with either dwarf or conventional plant height and subjected to high throughput sequencing analysis via mutation mapping (MutMap). The dwarf mutation was mapped to a 0.6 Mb interval of B. napus chromosome C05. Candidate gene analysis revealed that one SNP causing an amino acid change in the domain II of Bna.IAA7.C05 may contribute to the dwarf phenotype. This is consistent with the phenotype of a gain-of-function indole-3-acetic acid (iaa) mutant in Bna.IAA7.C05 reported recently. GO and KEGG analysis of RNA-seq data revealed the down-regulation of auxin related genes, including many other IAA and small up regulated response (SAUR) genes, in the dwarf mutant. Conclusion Our studies characterize a new allele of Bna.IAA7.C05 responsible for the dwarf mutant generated from tissue culture. This may provide a valuable genetic resource for breeding for lodging resistance and compact plant stature in B. napus.

scholarly journals A mutation in LacDWARF1 results in a GA-deficient dwarf phenotype in sponge gourd (Luffa acutangula)

2021 ◽  
Author(s):  
Gangjun Zhao ◽  
Caixia Luo ◽  
Jianning Luo ◽  
Junxing Li ◽  
Hao Gong ◽  
...  
Keyword(s):  
Gene Annotation ◽  
Recessive Gene ◽  
Genomic Region ◽  
Dwarf Mutant ◽  
Rna Seq ◽  
Dwarf Phenotype ◽  
Sponge Gourd ◽  
Response To Stress ◽  
Luffa Acutangula ◽  
Generation Sequencing

Abstract Key message A dwarfism gene LacDWARF1 was mapped by combined BSA-Seq and comparative genomics analyses to a 65.4 kb physical genomic region on chromosome 05. Abstract Dwarf architecture is one of the most important traits utilized in Cucurbitaceae breeding because it saves labor and increases the harvest index. To our knowledge, there has been no prior research about dwarfism in the sponge gourd. This study reports the first dwarf mutant WJ209 with a decrease in cell size and internodes. A genetic analysis revealed that the mutant phenotype was controlled by a single recessive gene, which is designated Lacdwarf1 (Lacd1). Combined with bulked segregate analysis and next-generation sequencing, we quickly mapped a 65.4 kb region on chromosome 5 using F2 segregation population with InDel and SNP polymorphism markers. Gene annotation revealed that Lac05g019500 encodes a gibberellin 3β-hydroxylase (GA3ox) that functions as the most likely candidate gene for Lacd1. DNA sequence analysis showed that there is an approximately 4 kb insertion in the first intron of Lac05g019500 in WJ209. Lac05g019500 is transcribed incorrectly in the dwarf mutant owing to the presence of the insertion. Moreover, the bioactive GAs decreased significantly in WJ209, and the dwarf phenotype could be restored by exogenous GA3 treatment, indicating that WJ209 is a GA-deficient mutant. All these results support the conclusion that Lac05g019500 is the Lacd1 gene. In addition, RNA-Seq revealed that many genes, including those related to plant hormones, cellular process, cell wall, membrane and response to stress, were significantly altered in WJ209 compared with the wild type. This study will aid in the use of molecular marker-assisted breeding in the dwarf sponge gourd.

scholarly journals Main Effect QTL with Dominance Determines Heterosis for Dynamic Plant Height in Upland Cotton

2016 ◽  
Vol 6 (10) ◽  
pp. 3373-3379 ◽  
Author(s):  
Lianguang Shang ◽  
Lingling Ma ◽  
Yumei Wang ◽  
Ying Su ◽  
Xiaocui Wang ◽  
...  
Keyword(s):  
Plant Height ◽  
Upland Cotton ◽  
Dynamic Plant ◽  
Main Effect

scholarly journals Reference transcriptome assembly and annotation for perennial ryegrass

Genome ◽  
2017 ◽  
Vol 60 (12) ◽  
pp. 1086-1088 ◽  
Author(s):  
Hiroshi Shinozuka ◽  
Noel O.I. Cogan ◽  
German C. Spangenberg ◽  
John W. Forster
Keyword(s):  
Perennial Ryegrass ◽  
Transcriptome Assembly ◽  
Genotyping By Sequencing ◽  
Whole Genome Sequence ◽  
Grass Species ◽  
Rna Seq ◽  
Pasture Grass ◽  
Tissue Samples ◽  
Genome Sequence Assembly ◽  
Transcriptome Resource

RNA-Seq methodology has been used to generate a comprehensive transcriptome sequence resource for perennial ryegrass, an important temperate pasture grass species. A total of 931 547 255 reads were obtained from libraries corresponding to 19 distinct tissue samples, including both vegetative and reproductive stages of development. Assembly of data generated a final filtered reference set of 48 713 contigs and scaffolds. The transcriptome resource will support whole genome sequence assembly, comparative genomics, implementation of genotyping-by-sequencing (GBS) methods based on transcript sampling, and identification of candidate genes for multiple biological functions.

scholarly journals Population Structure and Association Analysis of Bolting, Plant Height, and Leaf Erectness in Spinach

HortScience ◽  
2016 ◽  
Vol 51 (5) ◽  
pp. 481-486 ◽  
Author(s):  
Jessica Chitwood ◽  
Ainong Shi ◽  
Beiquan Mou ◽  
Michael Evans ◽  
John Clark ◽  
...  
Keyword(s):  
Linear Model ◽  
Plant Height ◽  
Spinacia Oleracea ◽  
Genotyping By Sequencing ◽  
Mixed Linear Model ◽  
Snp Markers ◽  
Structured Populations ◽  
United States Department ◽  
Nucleotide Polymorphisms ◽  
Single Marker

Spinach (Spinacia oleracea L.) is an important vegetable worldwide with high nutritional and health-promoting compounds. Bolting is an important trait to consider to grow spinach in different seasons and regions. Plant height and leaf erectness are important traits for machine harvesting. Breeding slow bolting, taller, and more erect spinach cultivars is needed for improved spinach production. A total of 288 United States Department of Agriculture (USDA) spinach accessions were used as the association panel in this research. Single-nucleotide polymorphisms (SNPs) discovered through genotyping by sequencing (GBS) were used for genotyping. Two structured populations and the admixtures were inferred for the 288 spinach accession panel using STRUCTURE and MEGA. Association mapping was conducted using single-marker regression (SMR) in QGene, and general linear model (GLM) and mixed linear model (MLM) built in TASSEL. Three SNP markers, AYZV02001321_398, AYZV02041012_1060, and AYZV02118171_95 were identified to be associated with bolting. Eight SNP markers, AYZV02014270_540, AYZV02250508_2162, AYZV02091523_19842, AYZV02141794_376, AYZV02077023_64, AYZV02210662_2532, AYZV02153224_2197, and AYZV02003975_248 were found to be associated with plant height. Four SNP markers, AYZV02188832_229, AYZV02219088_79, AYZV02030116_256, and AYZV02129827_197 were associated with erectness. These SNP markers may provide breeders with a tool in spinach molecular breeding to select spinach bolting, plant height, and erectness through marker-assisted selection (MAS).

scholarly journals Yield and some agronomic parameters of upland cotton as affected by planting dates

2020 ◽  
Vol 2 (1) ◽  
pp. 37
Author(s):  
Waqas Ahmed Lashari ◽  
Salma Naimatullah ◽  
Hamza Afzal
Keyword(s):  
Plant Height ◽  
Upland Cotton ◽  
Planting Date ◽  
Research Station ◽  
Cotton Yield ◽  
Seed Cotton ◽  
Planting Dates ◽  
Seed Cotton Yield ◽  
Average Maximum ◽  
Boll Weight

A field experiment was conducted at ICI Research Farm, Multan to evaluate the effect of different sowing dates on plant height, number of monopodia, number of sympodia, number of bolls per plant, boll weight, seed cotton yield kg/ha of two upland cotton varieties (ICI-2121 and ICI-2424) developed by ICI Pakistan Limited, Multan against a standard check variety IUB-2013 during 2019, and 2020 years.  These varieties were planted on 1st April, 15th April, 1st May, 15th May, 1st June, and 15th June, at ICI Cotton Research Station, 19-Kasi Vehari Road, Multan.  Results revealed that statistically highly significant differences in planting dates were observed for all the parameters studied except number of monopodial branches and boll weight which depicted non-significant differences. Regarding varieties and interaction between varieties and planting times, similar trend of statistical differences was observed. As regards to planting dates, generally, all the parameters under study showed their maximum performance when crop was planted on 1st May followed by 1st April planting date, whereas, minimum performance of the parameters was recorded when the crop was planted on 15th June followed by 1st June. Regarding varietal performance, on an average, maximum plant height (146cm) was observed in ICI-2121 followed by IUB-2013. Same trend of performance of varieties regarding number of monopodia and sympodia per plant was observed.  Regarding average number of bolls per plant in different varieties, it was observed that ICI-2121 produced maximum (32 bolls) followed by ICI-2424 (31 bolls) and IUB-2013 (28 bolls) irrespective of planting dates. The same trend of varietal performance regarding boll weight was recorded. When seed cotton yield (kg/ha) was evaluated, on an average of varieties, ICI-2121 produced maximum seed cotton yield (1228 kg/ha) followed by ICI-2424 and IUB-2013 which produced 1147 and 1046 kg/ha seed cotton yield respectively irrespective of planting dates. It was concluded that under agro-climatic conditions of Multan, 1st May planting date was evaluated as optimum cotton sowing time. Before or after 1st May, this study does not recommend growing cotton in this particular zone.  Among cotton varieties, ICI-2121 is recommended for sowing under this planting time being producing higher yields.

scholarly journals Transcriptome Profiling Provides Insights into Molecular Mechanism in Peanut Semi-dwarf Mutant

2020 ◽  
Author(s):  
Fengdan Guo ◽  
Junjie Ma ◽  
Lei Hou ◽  
Suhua Shi ◽  
Jinbo Sun ◽  
...  
Keyword(s):  
Molecular Mechanism ◽  
Plant Height ◽  
Molecular Mechanisms ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Main Stem ◽  
Differentially Expressed ◽  
Dwarf Mutant ◽  
Mature Stage ◽  
Stem Height

Abstract Background: Plant height, mainly decided by main stem height, is the major agronomic trait and closely correlated to crop yield. A number of studies had been conducted on model plants and crops to understand the molecular and genetic basis of plant height. However, little is known on the molecular mechanisms of peanut main stem height. Results: In this study, a semi-dwarf peanut mutant was identified from 60 Co γ-ray induced mutant population and designated as semi-dwarf mutant 2 ( sdm2 ). The height of sdm2 was only 59.3% of its wild line Fenghua 1 (FH1) at the mature stage. The sdm2 has less internode number and short internode length to compare with FH1. Gene expression profiles of stem and leaf from both sdm2 and FH1 were analyzed using high throughput RNA sequencing. The differentially expressed genes (DEGs) were involved in hormone biosynthesis and signaling pathways, cell wall synthetic and metabolic pathways. BR, GA and IAA biosynthesis and signal transduction pathways were significantly enriched. The expression of several genes in BR biosynthesis and signaling were found to be significantly down-regulated in sdm2 as compared to FH1. Many transcription factors encoding genes were identified as DEGs. Conclusions: A large number of genes were found differentially expressed between sdm2 and FH1. These results provide useful information for uncovering the molecular mechanism regulating peanut stem height. It could facilitate identification of causal genes for breeding peanut varieties with semi-dwarf phenotype.

scholarly journals Deciphering Rubber Tree Growth Using Network-Based Multi Omics Approaches

2021 ◽  
Author(s):  
Felipe Roberto Francisco ◽  
Alexandre Hild Aono ◽  
Carla Cristina da Silva ◽  
Paulo de Souza Gon&ccedilalves ◽  
Erivaldo Jos&eacute Scaloppi J&uacutenior ◽  
...  
Keyword(s):  
Plant Growth ◽  
Tree Growth ◽  
Association Studies ◽  
Rubber Tree ◽  
Genotyping By Sequencing ◽  
Tree Breeding ◽  
Genome Wide Association Studies ◽  
Rna Seq ◽  
Large Tree ◽  
Improvement Programs

Hevea brasiliensis (rubber tree) is a large tree species of the Euphorbiaceae family with inestimable economic importance. Rubber tree breeding programs currently aim to improve growth and production, and the use of early genotype selection technologies can accelerate such processes, mainly with the incorporation of genomic tools, such as marker-assisted selection (MAS). However, few quantitative trait loci (QTLs) have been used successfully in MAS for complex characteristics. Recent research shows the efficiency of genome-wide association studies (GWAS) for locating QTL regions in different populations. In this way, the integration of GWAS, RNA-sequencing (RNA-Seq) methodologies, coexpression networks and enzyme networks can provide a better understanding of the molecular relationships involved in the definition of the phenotypes of interest, supplying research support for the development of appropriate genomic based strategies for breeding. In this context, this work presents the potential of using combined multiomics to decipher the mechanisms of genotype and phenotype associations involved in the growth of rubber trees. Using GWAS from a genotyping-by-sequencing (GBS) Hevea population, we were able to identify molecular markers in QTL regions with a main effect on rubber tree plant growth under constant water stress. The underlying genes were evaluated and incorporated into a gene coexpression network modelled with an assembled RNA-Seq-based transcriptome of the species, where novel gene relationships were estimated and evaluated through in silico methodologies, including an estimated enzymatic network. From all these analyses, we were able to estimate not only the main genes involved in defining the phenotype but also the interactions between a core of genes related to rubber tree growth at the transcriptional and translational levels. This work was the first to integrate multiomics analysis into the in-depth investigation of rubber tree plant growth, producing useful data for future genetic studies in the species and enhancing the efficiency of the species improvement programs.

scholarly journals Genotyping by sequencing of 393 Sorghum bicolor BTx623 × IS3620C recombinant inbred lines improves sensitivity and resolution of QTL detection

2018 ◽  
Author(s):  
WenQian Kong ◽  
Changsoo Kim ◽  
Dong Zhang ◽  
Hui Guo ◽  
Xu Tan ◽  
...  
Keyword(s):  
Flowering Time ◽  
Plant Height ◽  
Recombinant Inbred ◽  
Recombinant Inbred Lines ◽  
Genotyping By Sequencing ◽  
Snp Markers ◽  
Ril Population ◽  
Trait Locus ◽  
Number Of Individuals ◽  
Syntenic Regions

AbstractWe describe a genetic map with a total of 381 bins of 616 genotyping by sequencing (GBS)-based SNP markers in a F6-F8 recombinant inbred line (RIL) population of 393 individuals derived from crossing S. bicolor BTx623 to S. bicolor IS3620C, a guinea line substantially diverged from BTx623. Five segregation distorted regions were found with four showing enrichment for S. bicolor alleles, suggesting possible selection during formation of this RIL population. A quantitative trait locus (QTL) study with this number of individuals, tripled relative to prior studies of this cross, provided resources, validated previous findings, and demonstrated improved power to detect plant height and flowering time related QTLs relative to other published studies. An unexpected low correlation between flowering time and plant height permitted us to separate QTLs for each trait and provide evidence against pleiotropy. Ten non-random syntenic regions conferring QTLs for the same trait suggest that those QTLs may represent alleles at genes functioning in the same manner since the 96 million year ago genome duplication that created these syntenic relationships, while syntenic regions conferring QTLs for different trait may suggest sub-functionalization after duplication. Collectively, this study provides resources for marker-assisted breeding, as well as a framework for fine mapping and subsequent cloning of major genes for important traits such as plant height and flowering time in sorghum.

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