scholarly journals Candidate Gene, SmCPR1, Encoding CPR1 Related to Plant Height of the Eggplant Dwarf Mutant dwf

Horticulturae ◽  
2021 ◽  
Vol 7 (7) ◽  
pp. 196
Author(s):  
Yang Lu ◽  
Shuangxia Luo ◽  
Na Li ◽  
Qiang Li ◽  
Wenchao Du ◽  
...  
Keyword(s):  
Candidate Gene ◽  
Bulked Segregant Analysis ◽  
Economic Value ◽  
Recessive Gene ◽  
Dwarf Mutant ◽  
Mutant Library ◽  
Vegetable Crop ◽  
Crop Breeding ◽  
Ethyl Methyl ◽  
Methyl Sulfonate

Eggplant is a vegetable crop with high economic value that is cultivated worldwide. The dwarf mutant is an important germplasm material that has been extensively used in crop breeding. However, no eggplant dwarf mutants have been reported, and little is known regarding the genes responsible for dwarfism in eggplant. In this study, we isolated an eggplant dwarf mutant (dwf) from an ethyl methyl sulfonate (EMS)-induced mutant library. Genetic analysis revealed that dwf was caused by a single recessive gene. A candidate gene SmCPR1, encoding cytochrome P450 reductases (CPR1), was identified by bulked segregant analysis (BSA). Mutation from G to A at 8216 bp of SmCPR1 resulted in mutation of the amino acid from valine to isoleucine. The results of KASP and Sanger sequencing further support the conclusion that SmCPR1 is a candidate gene responsible for the dwarfism of dwf. Moreover, the activity of SmCPR1 was significantly increased in dwf, which might be a response to dwarfism in dwf.

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 Fine Mapping and Candidate Gene Identification of a White Flower Gene BrWF3 in Chinese Cabbage (Brassica rapa L. ssp. pekinensis)

2021 ◽  
Vol 12 ◽  
Author(s):  
Shuangjuan Yang ◽  
Xinxin Tian ◽  
Zhiyong Wang ◽  
Xiaochun Wei ◽  
Yanyan Zhao ◽  
...  
Keyword(s):  
Candidate Gene ◽  
Chinese Cabbage ◽  
Fine Mapping ◽  
Protein Function ◽  
Recessive Gene ◽  
Flower Color ◽  
White Flower ◽  
Transmission Electron Microscopy Analysis ◽  
Electron Microscopy Analysis ◽  
Xanthophyll Esters

Flower color is an important trait in plants. However, genes responsible for the white flower trait in Chinese cabbage are rarely reported. In this study, we constructed an F2 population derived from the Y640-288 (white flower) and Y641-87 (yellow flower) lines for the fine mapping of the white flower gene BrWF3 in Chinese cabbage. Genetic analysis indicated that BrWF3 was controlled by a single recessive gene. Using BSA-seq and KASP assays, BrWF3 was fine-mapped to an interval of 105.6 kb. Functional annotation, expression profiling, and sequence variation analyses confirmed that the AtPES2 homolog, Bra032957, was the most likely candidate gene for BrWF3. Carotenoid profiles and transmission electron microscopy analysis suggested that BrWF3 might participate in the production of xanthophyll esters (particularly violaxanthin esters), which in turn disrupt chromoplast development and the formation of plastoglobules (PGs). A SNP deletion in the third exon of BrWF3 caused the loss of protein function, and interfered with the normal assembly of PGs, which was associated with reduced expression levels of genes involved in carotenoid metabolism. Furthermore, we developed and validated the functional marker TXBH83 for BrWF3. Our results provide insight into the molecular mechanism underlying flower color pigmentation and reveal valuable information for marker-assisted selection (MAS) breeding in Chinese cabbage.

Fine mapping and candidate gene analysis of LM3, a novel lesion mimic gene in rice

Biologia ◽  
2013 ◽  
Vol 68 (1) ◽  
Author(s):  
Yuxiang Zeng ◽  
Liangyong Ma ◽  
Zhijuan Ji ◽  
Zhihua Wen ◽  
Ximing Li ◽  
...  
Keyword(s):  
Candidate Gene ◽  
Target Gene ◽  
Recessive Gene ◽  
Coding Region ◽  
Uroporphyrinogen Decarboxylase ◽  
Single Nucleotide ◽  
Lesion Mimic ◽  
Indel Markers ◽  
Fourth Exon ◽  
Simple Sequence

AbstractA rice lesion mimic mutant, lm3, was obtained by the mutagenesis of an indica cultivar, 93-11, using γ-ray radiation. Brownish lesions appeared on the leaves of lm3 at the young seedling stage and persisted until the ripening stage. The lm3 mutant was characterised by a shorter plant height and delayed heading compared with the wild-type 93-11. A genetic analysis indicated that the lesion mimic phenotype was controlled by a single recessive gene. Using simple sequence repeat (SSR) markers, the target gene LM3 was first located between marker RM5748 and RM14906 on chromosome 3. We then developed Insertion-Deletion (InDel) markers to fine-map LM3, and the locus was localised to a 29 kb region defined by two InDel markers, In12571 and In12600. Five ORFs were predicted in the candidate region, and DNA sequencing detected a single-nucleotide polymorphism (SNP) in the coding region of LOC Os03g21900. The SNP in the fourth exon (C in 93-11; T in lm3) of LOC_Os03g21900 results in the substitution of a proline (P) with a serine (S) at the 140th amino acid of the deduced uroporphyrinogen decarboxylase protein. We did not detect polymorphisms in the other predicted ORF regions between lm3 and 93-11. These results suggest that LOC_Os03g21900 is the most likely candidate gene for LM3.

Rapid mapping of a chlorina mutant gene cn-A1 in hexaploid wheat by bulked segregant analysis and single nucleotide polymorphism genotyping arrays

2019 ◽  
Vol 70 (10) ◽  
pp. 827 ◽  
Author(s):  
H. B. Jiang ◽  
N. Wang ◽  
J. T. Jian ◽  
C. S. Wang ◽  
Y. Z. Xie
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Single Nucleotide Polymorphism Array ◽  
Bulked Segregant Analysis ◽  
Recessive Gene ◽  
Mutant Gene ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Chlorophyll Metabolism ◽  
Specific Pcr ◽  
Leaf Mutant

The yellow–green leaf mutant can be exploited in photosynthesis and plant development research. A Triticum aestivum mutant with the chlorina phenotype, here called B23, was produced by treatment with the chemical mutagen sodium azide. This B23 mutant showed significantly lower chlorophyll content than wild-type Saannong33, and its chloroplast structure was abnormal. All its yield-related traits, except for the number of spikes per plant, were also significantly decreased. Genetic analysis confirmed that the mutant phenotype was controlled by a recessive gene, here designated cn-A1. Using bulked segregant analysis and the wheat 660K single nucleotide polymorphism array, the cn-A1 gene was mapped to chromosome 7AL, and 11 polymorphic markers were developed. Further analysis showed that cn-A1 was located in a 1.1-cM genetic region flanked by Kompetitive allele specific PCR (KASP) markers 660K-7A12 and 660K-7A20, which corresponded to a physical interval of 3.48 Mb in T. aestivum cv. Chinese Spring chromosome 7AL containing 47 predicted genes with high confidence. These results are expected to accelerate the process of cloning the cn-A1 gene and facilitate understanding of the mechanisms underlying chlorophyll metabolism and chloroplast development in wheat.

scholarly journals Mapping and Identifying a Candidate Gene Plr4, a Recessive Gene Regulating Purple Leaf in Rice, by Using Bulked Segregant and Transcriptome Analysis with Next-Generation Sequencing

2019 ◽  
Vol 20 (18) ◽  
pp. 4335 ◽  
Author(s):  
Ju Gao ◽  
Gaoxing Dai ◽  
Weiyong Zhou ◽  
Haifu Liang ◽  
Juan Huang ◽  
...  
Keyword(s):  
Molecular Mechanisms ◽  
Anthocyanin Biosynthesis ◽  
Bulked Segregant Analysis ◽  
Recessive Gene ◽  
Leaf Traits ◽  
Anthocyanin Synthesis ◽  
Genetic Characteristics ◽  
Specific Organ ◽  
Flower Organs ◽  
Purple Leaf

The anthocyanin biosynthesis of rice is a major concern due to the potential nutritional value. Purple appears in various organs and tissues of rice such as pericarp, flower organs, leaves, leaf sheaths, internodes, ligules, apex, and stigma. At present, there are many studies on the color of rice pericarp, but the gene and mechanism of other organs such as leaves are still unclear, and the gene regulatory network of specific organ coloring has not been systematically understood. In this study, genetic analysis demonstrated that the purple leaf traits of rice were regulated by a recessive gene. The green leaf cultivar Y58S and purple leaf cultivar XianHongB were used to construct the mapping population. A set of near isogenicline (NIL) (BC3F1) was bred via crossing and back-crossing. The generations of BC3F2 appeared to separate four phenotypes, pl1, pl2, pl3, and pl4, due to the occurrence of a purple color in different organs. We constructed three bulked segregant analysis (BSA) pools (pl1–pl2, pl1–pl3, and pl1–pl4) by using the separated generations of BC3F5 and mapped the purple leaf gene plr4 to the vicinity of 27.9–31.1 Mb on chromosome 4. Subsequently, transcriptome sequencing (RNA-Seq) for pl3 and pl2 was used to analyze the differentially expressed genes in the localization interval, where 12 unigenes exhibited differential expression in which two genes (Os04g0577800, Os04g0616400) were downregulated. The two downregulated genes (Os04g0577800 and Os04g0616400) are possible candidate genes because of the recessive genetic characteristics of the purple leaf genes. These results will facilitate the cloning of plr4 and illustrate the molecular mechanisms of the anthocyanin synthesis pathway.

scholarly journals Fine-Mapping And Identification of A Candidate Gene Controlling Seed Coat Color In Melon (Cucumis Melo L. Var. Chinensis Pangalo)

2021 ◽  
Author(s):  
Zhicheng Hu ◽  
Xueyin Shi ◽  
Xuemiao Chen ◽  
Jing Zheng ◽  
Aiai Zhang ◽  
...  
Keyword(s):  
Candidate Gene ◽  
Seed Coat ◽  
Coat Color ◽  
Bulked Segregant Analysis ◽  
Dominant Gene ◽  
Seed Coat Color ◽  
Gene Encoding ◽  
Yellow Seed ◽  
Homeobox Protein ◽  
Yellow Seed Coat

Abstract Seed coat color is related to flavonoid content which is closely related to seed dormancy. According to the genetic analysis of a six-generation population derived from two parents (IC2508 with a yellow seed coat and IC2518 with a brown seed coat), we discovered that the yellow seed coat trait in melon was controlled by a single dominant gene, named CmBS-1. Bulked segregant analysis sequencing (BSA-Seq) revealed that the gene was located at 11,860,000–15,890,000 bp (4.03 Mb) on Chr 6. The F2 population was genotyped using insertion-deletions (InDels), from which cleaved amplified polymorphic sequence (dCAPS) markers were derived to construct a genetic map. The gene was then fine-mapped to a 233.98 kb region containing 12 genes. Based on gene sequence analysis with two parents, we found that the MELO3C019554 gene encoding a homeobox protein (PHD transcription factor) had a nonsynonymous single nucleotide polymorphism (SNP) mutation in the coding sequence (CDS), and the SNP mutation resulted in the conversion of an amino acid (A→T) at residue 534. In addition, MELO3C019554 exhibited lower relative expression levels in the yellow seed coat than in the brown seed coat. Furthermore, we found that MELO3C019554 was related to 12 flavonoid metabolites. Thus, we predicted that MELO3C019554 is a candidate gene controlling seed coat color in melon. The study lays a foundation for further cloning projects and functional analysis of this gene, as well as marker-assisted selection breeding.

scholarly journals Genetic Analysis and Related Gene Primary Mapping of Heat Stress Tolerance in Cucumber Using Bulked Segregant Analysis

HortScience ◽  
2019 ◽  
Vol 54 (3) ◽  
pp. 423-428
Author(s):  
Min Wang ◽  
Wenrui Liu ◽  
Biao Jiang ◽  
Qingwu Peng ◽  
Xiaoming He ◽  
...  
Keyword(s):  
Heat Stress ◽  
Genetic Analysis ◽  
Candidate Genes ◽  
High Temperatures ◽  
Genomic Sequence ◽  
Bulked Segregant Analysis ◽  
Recessive Gene ◽  
Chromosome 1 ◽  
Isolation And Characterization ◽  
Indel Markers

Heat stress (HS) negatively influences plant development and growth, especially production and quality. Cucumber is a widely cultivated plant in the gourd family Cucurbitaceae that is often exposed to high temperatures during summer and protected cultivation. In this study, we performed whole-genome re-sequencing of two pools, one heat-tolerant and one heat-sensitive, of the F2 population derived from L-9 (heat-resistant) and A-16 (heat-sensitive). The genetic analysis showed that the heat resistance of L-9 cucumber seedlings was controlled by a single recessive gene. By combining bulked segregant analysis (BSA) technology, the crucial gene related to HS was preliminarily mapped to a 1.08-Mb region on chromosome 1. To fine-map the locus, Indel markers were designed according to the genomic sequence. Finally, the gene was narrowed to a 550-kb region flanked by two Indel markers, namely Indel-H90 and Indel-H224, that contained 56 candidate genes. Re-sequencing results indicated that 10 candidate genes among the 56 in the candidate region showed single base pair differences in the exons. Quantitative reverse-transcription polymerase chain reaction showed that 6 genes among the 10 candidate genes were significantly decreased when exposed to high temperatures. These results not only were useful for the isolation and characterization of the key genes involved in HS but also provided a basis for understanding the mechanism of heat tolerance regulation.

scholarly journals Genetic mapping and candidate gene analysis for melon resistance to Phytophthora capsici

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Pingyong Wang ◽  
Xiaojun Xu ◽  
Guangwei Zhao ◽  
Yuhua He ◽  
Chong Hou ◽  
...  
Keyword(s):  
Candidate Gene ◽  
Cucumis Melo ◽  
Bulked Segregant Analysis ◽  
Phytophthora Capsici ◽  
Expression Patterns ◽  
Dominant Gene ◽  
Resistance Mechanism ◽  
Receptor Kinase ◽  
Caps Marker ◽  
Mutation Site

AbstractPhytophthora blight is one of the most serious diseases affecting melon (Cucumis melo) production. Due to the lack of highly resistant germplasms, the progress on disease-resistant research is slow. To understand the genetics of melon resistance to Phytophthora capsici, an F2 population containing 498 individuals was developed by crossing susceptible line E31 to highly resistant line ZQK9. Genetic analysis indicated that the resistance in ZQK9 was controlled by a dominant gene, tentatively named MePhyto. Through bulked-segregant analysis (BSA-Seq) and chromosome walking techniques, the MePhyto gene was mapped to a 52.44 kb interval on chromosome 12. In this region, there were eight genes and their expression patterns were validated by qRT-PCR. Among them, one wall-associated receptor kinase (WAK) gene MELO3C002430 was significantly induced in ZQK9 after P. capsici inoculation, but not in E31. Based on the non-synonymous mutation site in MELO3C002430, a cleaved amplified polymorphic sequence (CAPS) marker, CAPS2430, was developed and this maker was co-segregated with MePhyto in both F2 population and a collection of 36 melon accessions. Thus MELO3C002430 was considered as the candidate gene and CAPS2430 was a promising marker for marker-assisted selection (MAS) in breeding. These results lay a foundation for revealing the resistance mechanism of melon to P. capsici.

BSA‑Seq and Genetic Mapping Reveals AhRt2 as a Candidate Gene Responsible for Red Testa of Peanut

2021 ◽  
Author(s):  
Kun Zhang ◽  
Mei Yuan ◽  
Han Xia ◽  
Liangqiong He ◽  
Jing Ma ◽  
...  
Keyword(s):  
Candidate Gene ◽  
Linkage Mapping ◽  
Sequence Variation ◽  
Diagnostic Marker ◽  
Recessive Gene ◽  
Single Recessive Gene ◽  
The Third ◽  
Important Trait ◽  
Testa Color ◽  
Insight Into

Abstract Testa color is an important trait of peanut (Arachis hypogaea L.). Peanuts with red testa are rich in anthocyanin, are very popular with consumers. However, genes responsible for the red testa trait in peanut are rarely reported. In order to fine map red testa gene, two F4 populations were constructed through the cross of YZ9102 (pink testa) with ZH12 (red testa) and Zhanhong2 (red testa). Genetic analysis indicated that red testa was controlled by a single recessive gene, and named as AhRt2 (Red testa gene 2). Using BSA-seq approach, AhRt2 was preliminary identified in chromosome 12, and further mapped to a 530-kb interval using 220 recombinant lines through linkage mapping. Functional annotation, expression profiling, and sequence variation analyses confirmed that the anthocyanin reductase (ANR), Arahy.IK60LM, was the most likely candidate gene for AhRt2. A SNP in the third exon of AhRt2 changed the encoding amino acids, was associated with red testa of peanut. In addition, a closely linkaged molecular marker to red testa trait was developed. Our result provide insight into the molecular mechanism underlying peanut testa color and provide valuable diagnostic marker for marker-assisted selected (MAS) breeding in peanut.

Sorting for secreted molecule production using a biosensor-in-microdroplet approach

2021 ◽  
Vol 118 (36) ◽  
pp. e2106818118
Author(s):  
Emily K. Bowman ◽  
James M. Wagner ◽  
Shuo-Fu Yuan ◽  
Matthew Deaner ◽  
Claire M. Palmer ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Saccharomyces Cerevisiae ◽  
Cell Type ◽  
Guide Rna ◽  
E Coli ◽  
Ethyl Methyl ◽  
Methyl Sulfonate ◽  
Acid Lactone ◽  
Mix And Match ◽  
Molecule Production

Sorting large libraries of cells for improved small molecule secretion is throughput limited. Here, we combine producer/secretor cell libraries with whole-cell biosensors using a microfluidic-based screening workflow. This approach enables a mix-and-match capability using off-the-shelf biosensors through either coencapsulation or pico-injection. We demonstrate the cell type and library agnostic nature of this workflow by utilizing single-guide RNA, transposon, and ethyl-methyl sulfonate mutagenesis libraries across three distinct microbes (Escherichia coli, Saccharomyces cerevisiae, and Yarrowia lipolytica), biosensors from two organisms (E. coli and S. cerevisiae), and three products (triacetic acid lactone, naringenin, and L-DOPA) to identify targets improving production/secretion.

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