scholarly journals Rapid identification of a candidate gene related to fiber strength using a superior chromosome segment substitution line from Gossypium hirsutum ×Gossypium barbadense via bulked segregant RNA-sequencing

2019 ◽  
Author(s):  
Qi Zhang ◽  
Pengtao Li ◽  
Aiying Liu ◽  
Quanwei Lu ◽  
Juwu Gong ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Rna Sequencing ◽  
Fiber Strength ◽  
Rapid Identification ◽  
Differentially Expressed ◽  
Chromosome Segment ◽  
Strength Development ◽  
Recurrent Parent ◽  
Allelic Polymorphism ◽  
Segment Substitution

Abstract Gossypium is the most widely cultivated commercial crop producing natural fiber around the world, and fiber strength principally determined during the secondary wall thickening period is a critical trait for fiber quality. Based on the developed BC 5 F 3:5 CSSLs (chromosome segment substitution lines) from G. hisutum CCRI36 × G. barbadense Hai1, the superior MBI9915 was chosen to construct the secondary segregated population BC 7 F 2 with its recurrent parent CCRI36, which was subjected to Bulk segregant RNA-sequencing (BSR-seq) for rapid identification of candidate genes related to fiber strength. Four fiber-transcriptome libraries were separately constructed and sequenced, including two parents (CCRI36 and MBI9915) and two extreme pools at 20 DPA (days post anathesis). Through multiple comparisons, 3742 DEGs (differentially expressed genes) and 3252 DEGs were separately identified between two parents and between two extreme pools, while 536 DEGs were overlapped between parent and extreme pool groups. A total of 831high-probability SNPs (single nucleotide polymorphism) were identified relevant to fiber strength between two extreme pools through allelic-polymorphism comparison in mRNA sequences, and 18 correlated regions with 1981 annotation genes were finally screened by linkage analysis with SNP-index method, of which including only 12 common genes differentially expressed both between two parents and two pools. Interesting, there was one correlated region consistent with the previous study with the same parents on chromosome A07 with 13-14 Mb, and one common DEG ( Gh_A07G0837 ) in the candidate region was identified in both parents and extreme pools, which has been reported to be involved in fiber strength development through regulating reactive oxygen species (ROS) activity. The reliability of BSR-seq results was validated by the quantitative real-time PCR (qRT-PCR) experiments on 5 DEGs at 20 DPA. This study focuses on bulked segregant analysis of the extreme pools from segregation population developed by superior CSSL and its recurrent parent, indicating that BSR-seq can be efficiently applied on rapid identification for candidate genes related to the significant quantitative traits, which provides valuable contributions for comprehension of fiber strength formation in cotton.

scholarly journals Identifying Candidate Genes for Hypoxia Adaptation of Tibet Chicken Embryos by Selection Signature Analyses and RNA Sequencing

Genes ◽  
2020 ◽  
Vol 11 (7) ◽  
pp. 823
Author(s):  
Xiayi Liu ◽  
Xiaochen Wang ◽  
Jing Liu ◽  
Xiangyu Wang ◽  
Haigang Bao
Keyword(s):  
Candidate Genes ◽  
Rna Sequencing ◽  
Differentially Expressed Genes ◽  
Gallus Gallus ◽  
Differentially Expressed ◽  
Tibet Plateau ◽  
Embryonic Liver ◽  
Selection Signature ◽  
Chicken Embryos ◽  
Hypoxia Adaptation

The Tibet chicken (Gallus gallus) lives on the Qinghai–Tibet Plateau and adapts to the hypoxic environment very well. The objectives of this study was to obtain candidate genes associated with hypoxia adaptation in the Tibet chicken embryos. In the present study, we used the fixation index (Fst) and cross population extended haplotype homozygosity (XPEHH) statistical methods to detect signatures of positive selection of the Tibet chicken, and analyzed the RNA sequencing data from the embryonic liver and heart with HISAT, StringTie and Ballgown for differentially expressed genes between the Tibet chicken and White leghorn (Gallus gallus, a kind of lowland chicken) embryos hatched under hypoxia condition. Genes which were screened out by both selection signature analysis and RNA sequencing analysis could be regarded as candidate genes for hypoxia adaptation of chicken embryos. We screened out 1772 genes by XPEHH and 601 genes by Fst, and obtained 384 and 353 differentially expressed genes in embryonic liver and heart, respectively. Among these genes, 89 genes were considered as candidate genes for hypoxia adaptation in chicken embryos. ARNT, AHR, GSTK1 and FGFR1 could be considered the most important candidate genes. Our findings provide references to elucidate the molecular mechanism of hypoxia adaptation in Tibet chicken embryos.

scholarly journals Analysis of Soybean Somatic Embryogenesis Using Chromosome Segment Substitution Lines and Transcriptome Sequencing

Genes ◽  
2019 ◽  
Vol 10 (11) ◽  
pp. 943
Author(s):  
Li ◽  
Cheng ◽  
Bai ◽  
Shi ◽  
Yu ◽  
...  
Keyword(s):  
Somatic Embryogenesis ◽  
Differentially Expressed Genes ◽  
Transcriptome Sequencing ◽  
Target Genes ◽  
Differentially Expressed ◽  
Chromosome Segment ◽  
Substitution Lines ◽  
Chromosome Segment Substitution Lines ◽  
Segment Substitution ◽  
Extreme Materials

Soybean is an important cash crop that is widely used as a source of vegetable protein and edible oil. The regeneration ability of soybean directly affects the application of biotechnology. In this study, we used the exogenous hormone 2,4-D to treat immature embryos. Different levels of somatic incidence were selected from the chromosome segment substitution lines (CSSLs) constructed by SN14 and ZYD00006. Transcriptome sequencing of extreme materials was performed, and 2666 differentially expressed genes were obtained. At the same time, a difference table was generated by combining the data on CSSL rearrangement. In the extreme materials, a total of 93 differentially expressed genes were predicted and were then analyzed by cluster analysis and Gene Ontology (GO) annotation. After screening and annotating the target genes, three differentially expressed genes with hormone pathways were identified. The expression patterns of the target genes were verified by real-time quantitative PCR (qRT-PCR). Haplotype polymorphism detection and linkage disequilibrium analysis were performed on the candidate gene Glyma.09g248200. This study provided more information on the regulation network of soybean somatic embryogenesis and regeneration processes, and further identified important genes in the soybean regeneration process and provided a theoretical basis for accelerating the application of biotechnology to soybean for improving its breeding efficiency.

scholarly journals Genome-Wide Association Study and Transcriptome Differential Expression Analysis of the Feather Rate in Shouguang Chickens

2020 ◽  
Vol 11 ◽  
Author(s):  
Xiayi Liu ◽  
Zhou Wu ◽  
Junying Li ◽  
Haigang Bao ◽  
Changxin Wu
Keyword(s):  
Differential Expression ◽  
Candidate Genes ◽  
Rna Sequencing ◽  
Expression Analysis ◽  
Differential Expression Analysis ◽  
Serine Phosphorylation ◽  
Differentially Expressed ◽  
Genome Wide Association ◽  
Sequencing Analysis ◽  
Genome Wide

The feather rate phenotype in chicks, including early-feathering and late-feathering phenotypes, are widely used as a sexing system in the poultry industry. The objective of this study was to obtain candidate genes associated with the feather rate in Shouguang chickens. In the present study, we collected 56 blood samples and 12 hair follicle samples of flight feathers from female Shouguang chickens. Then we identified the chromosome region associated with the feather rate by genome-wide association analysis (GWAS). We also performed RNA sequencing and analyzed differentially expressed genes between the early-feathering and late-feathering phenotypes using HISAT2, StringTie, and DESeq2. We identified a genomic region of 10.0–13.0 Mb of chromosome Z, which is statistically associated with the feather rate of Shouguang chickens at one-day old. After RNA sequencing analysis, 342 differentially expressed known genes between the early-feathering (EF) and late-feathering (LF) phenotypes were screened out, which were involved in epithelial cell differentiation, intermediate filament organization, protein serine kinase activity, peptidyl-serine phosphorylation, retinoic acid binding, and so on. The sperm flagellar 2 gene (SPEF2) and prolactin receptor (PRLR) gene were the only two overlapping genes between the results of GWAS and differential expression analysis, which implies that SPEF2 and PRLR are possible candidate genes for the formation of the chicken feathering phenotype in the present study. Our findings help to elucidate the molecular mechanism of the feather rate in chicks.

scholarly journals Revelation of candidate genes and molecular mechanism of reproductive seasonality in carp fish (Labeo rohita Ham) by RNA sequencing

2020 ◽  
Author(s):  
Sarika Jaiswal ◽  
Samiran Nandi ◽  
Mir Iquebal ◽  
Rahul Jasrotia ◽  
Sunita Patra ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Rna Sequencing ◽  
De Novo ◽  
Clock Genes ◽  
Labeo Rohita ◽  
Monsoon Season ◽  
Biological Clock ◽  
Differentially Expressed ◽  
Freshwater Aquaculture ◽  
Carp Fish

Abstract BackgroundCarp fish, rohu (Labeo rohita Ham) is important freshwater aquaculture species of South-East Asia having seasonal reproductive rhythm. There is no holistic study at transcriptome level revealing key candidate genes involved in such circannual rhythm regulated by biological clock genes (BCGs). Seasonality manifestation has two contrasting phases of reproduction, i.e., post-spawning regression and initiation of gonadal activity appropriate for discovery of associated candidate genes. It can be deciphered by RNA sequencing of tissues involved in BPGL (Brain-Pituitary-Gonad-Liver) axis controlling seasonality. How far such BCGs of this fish are evolutionarily conserved across different phyla is unknown. Such study can be of further use to enhance fish productivity as seasonality restricts seed production beyond monsoon season.ResultA total of ~150 Gb of transcriptomic data of four tissues viz., BPGL were generated using Illumina TruSeq. De-novo assembled BPGL tissues revealed 75554 differentially expressed transcripts, 115534 SSRs, 65584 SNPs, 514 pathways, 5379 transcription factors, 187 mature miRNA which regulates candidate genes represented by 1576 differentially expressed transcripts which are available in the form of web-genomic resources. Findings were validated by qPCR. This is first report in carp fish having 32 BCGs found widely conserved in fish, amphibian, reptile, birds, prototheria, marsupials and placental mammals. This is due to universal mechanism of rhythmicity in response to environment and earth rotation having adaptive and reproductive significance.ConclusionThis study elucidates evolutionary conserved mechanism of photo-periodism sensing, neuroendocrine secretion, metabolism and yolk synthesis in liver, gonadal maturation, muscular growth with sensory and auditory perception in this fish. Study reveals fish as a good model for research on biological clock besides its relevance in reproductive efficiency enhancement.

QTL mapping for the number of branches and pods using wild chromosome segment substitution lines in soybean [Glycine max (L.) Merr.]

2014 ◽  
Vol 12 (S1) ◽  
pp. S172-S177 ◽  
Author(s):  
Qingyuan He ◽  
Hongyan Yang ◽  
Shihua Xiang ◽  
Wubing Wang ◽  
Guangnan Xing ◽  
...  
Keyword(s):  
Wild Soybean ◽  
Chromosome Segment ◽  
Yield Potential ◽  
Recurrent Parent ◽  
Substitution Lines ◽  
Phenotypic Data ◽  
Mapping Procedure ◽  
Positive Effects ◽  
Segment Substitution ◽  
Number Of Branches

Annual wild soybean characterized with more number of branches and pods may contain favourable exotic genes/alleles for improving the yield potential of cultivated soybeans. To evaluate the wild alleles/segments, the chromosome segment substitution line population SojaCSSLP3 comprising 158 lines with N24852 (wild) as the donor and NN1138-2 (cultivated) as the recurrent parent was tested under three environments. The phenotypic data along with 198 simple sequence repeat markers were analysed for qualitative trait loci (QTL)/segments associated with the number of branches on the main stem (BN) and number of pods per plant (PN) using the inclusive composite interval mapping procedure (RSTEP-LRT-ADD model) of ICIM version 3.0. The analysis was carried out for individual environments due to a significant G × E interaction. A total of eight QTL/segments associated with BN and eight QTL/segments associated with PN were detected under the three environments, with all the wild segments having positive effects. Among these, two QTL/segments for each of the two traits could be detected under two or three environments and three QTL/segments could be detected for both traits. Four QTL/segments associated with BN and one QTL/segment associated with PN were identified only in SojaCSSLP3, not reported for cultivated crosses in the literature. The detected wild segments may provide materials for further characterization, cloning and pyramiding of the alleles conferring the two traits.

scholarly journals Revelation of candidate genes and molecular mechanism of reproductive seasonality in female rohu (Labeo rohita Ham.) by RNA sequencing

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Sarika Jaiswal ◽  
Samiran Nandi ◽  
Mir Asif Iquebal ◽  
Rahul Singh Jasrotia ◽  
Sunita Patra ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Rna Sequencing ◽  
De Novo ◽  
Clock Genes ◽  
Labeo Rohita ◽  
Monsoon Season ◽  
Biological Clock ◽  
Differentially Expressed ◽  
Freshwater Aquaculture ◽  
Carp Fish

Abstract Background Carp fish, rohu (Labeo rohita Ham.) is important freshwater aquaculture species of South-East Asia having seasonal reproductive rhythm. There is no holistic study at transcriptome level revealing key candidate genes involved in such circannual rhythm regulated by biological clock genes (BCGs). Seasonality manifestation has two contrasting phases of reproduction, i.e., post-spawning resting and initiation of gonadal activity appropriate for revealing the associated candidate genes. It can be deciphered by RNA sequencing of tissues involved in BPGL (Brain-Pituitary-Gonad-Liver) axis controlling seasonality. How far such BCGs of this fish are evolutionarily conserved across different phyla is unknown. Such study can be of further use to enhance fish productivity as seasonality restricts seed production beyond monsoon season. Result A total of ~ 150 Gb of transcriptomic data of four tissues viz., BPGL were generated using Illumina TruSeq. De-novo assembled BPGL tissues revealed 75,554 differentially expressed transcripts, 115,534 SSRs, 65,584 SNPs, 514 pathways, 5379 transcription factors, 187 mature miRNA which regulates candidate genes represented by 1576 differentially expressed transcripts are available in the form of web-genomic resources. Findings were validated by qPCR. This is the first report in carp fish having 32 BCGs, found widely conserved in fish, amphibian, reptile, birds, prototheria, marsupials and placental mammals. This is due to universal mechanism of rhythmicity in response to environment and earth rotation having adaptive and reproductive significance. Conclusion This study elucidates evolutionary conserved mechanism of photo-periodism sensing, neuroendocrine secretion, metabolism and yolk synthesis in liver, gonadal maturation, muscular growth with sensory and auditory perception in this fish. Study reveals fish as a good model for research on biological clock besides its relevance in reproductive efficiency enhancement.

scholarly journals Fine Mapping of A QTL Locus (QNFSP07-1) And Analysis of Candidate Genes For Four-Seeded Pods In Soybean

2021 ◽  
Author(s):  
Yingying Li ◽  
Chunyan Liu ◽  
Nannan Wang ◽  
Zhanguo Zhang ◽  
Lilong Hou ◽  
...  
Keyword(s):  
Qtl Mapping ◽  
Candidate Genes ◽  
Developmental Stages ◽  
Gene Annotation ◽  
High Ratio ◽  
Recurrent Parent ◽  
Substitution Lines ◽  
Chromosome Segment Substitution Lines ◽  
Gene Map ◽  
Segment Substitution

Abstract The number of four-seeded pods is a quantitative trait in soybean [Glycine max (L.) Merr.] and is closely related to yield in terms of breeding. In this study, individuals with high ratio of four-seed pods which from chromosome segment substitution lines (CSSLs) that can be stably inherited were selected as the parent, and Suinong 14 (SN14) was used as recurrent parent to construct secondary mapping population via marker-assisted selection. The initial QTL mapping interval was 0.67 Mb and was located on Gm07. Based on the initial QTL mapping results, individuals that were heterozygous at the interval (36116118-37399738 bp) were screened, and the heterozygous individuals were subjected to inbreeding to obtain 13 F3 populations, with a target interval of 321 kb. Gene annotation was performed on the finely mapped interval, and 27 genes were obtained. Glyma.07G200900, Glyma.07G201200 were identified as candidate genes. qRT-PCR was used to measure the expression of the candidate genes at different developmental stages of soybean. The expression levels of the 2 candidate genes in terms of cell division (axillary buds, COTs, EMs) were higher than those in terms of cell expansion (MM, LM), and these genes play a positive regulatory role in the formation of four-seeded pods. Haplotype analysis shows that Glyma.07G201200 has two excellent haplotypes. Those results provide the information for gene map-based cloning and molecular marker assisted breeding of the number of four-seeded pod in soybean.

scholarly journals Fine Mapping of a Novel Major Quantitative Trait Locus, qPAA7, That Controls Panicle Apical Abortion in Rice

2021 ◽  
Vol 12 ◽  
Author(s):  
Xiaolei Wang ◽  
Lingfeng Li ◽  
Xiaotang Sun ◽  
Jie Xu ◽  
Linjuan Ouyang ◽  
...  
Keyword(s):  
Quantitative Trait Locus ◽  
Candidate Genes ◽  
Quantitative Trait ◽  
Gene Annotation ◽  
Functional Characterization ◽  
Recurrent Parent ◽  
Substitution Lines ◽  
Chromosome Segment Substitution Lines ◽  
Trait Locus ◽  
Segment Substitution

The panicle apical abortion (PAA) causes severe yield losses in rice production, but details about its development and molecular basis remain elusive. Here, we detected PAA quantitative trait loci (QTLs) in three environments using a set of chromosome segment substitution lines (CSSLs) that was constructed with indica Changhui121 as the recurrent parent and japonica Koshihikari as the donor parent. First, we identified a novel major effector quantitative trait locus, qPAA7, and selected a severe PAA line, CSSL176, which had the highest PAA rate among CSSLs having Koshihikari segments at this locus. Next, an F2 population was constructed from a cross between CSS176 and CH121. Using F2 to make recombinantion analysis, qPAA7 was mapped to an 73.8-kb interval in chromosome 7. Among nine candidate genes within this interval, there isn’t any known genes affecting PAA. According to the gene annotation, gene expression profile and alignment of genomic DNA, LOC_Os07g41220 and LOC_Os07g41280 were predicted as putative candidate genes of qPAA7. Our study provides a foundation for cloning and functional characterization of the target gene from this locus.

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