scholarly journals A High-Density SNP Genetic Map Construction Using ddRAD-Seq and Mapping of Capsule Shattering Trait in Sesame

2021 ◽  
Vol 12 ◽  
Author(s):  
Engin Yol ◽  
Merve Basak ◽  
Sibel Kızıl ◽  
Stuart James Lucas ◽  
Bulent Uzun
Keyword(s):  
Genetic Map ◽  
Low Cost ◽  
High Density ◽  
Chromosome 8 ◽  
Nucleotide Polymorphisms ◽  
Loss Of Function ◽  
Single Nucleotide ◽  
Breeding Programs ◽  
Map Construction ◽  
Flanking Region

The seed-bearing capsule of sesame shatters at harvest. This wildish trait makes the crop unsuitable for mechanized harvesting and also restricts its commercial potential by limiting the cultivation for countries that have no access to low-cost labor. Therefore, the underlying genetic basis of the capsule shattering trait is highly important in order to develop mechanization-ready varieties for sustainable sesame farming. In the present study, we generated a sesame F2 population derived from a cross between a capsule shattering cultivar (Muganli-57) and a non-shattering mutant (PI 599446), which was used to construct a genetic map based on double-digest restriction-site-associated DNA sequencing. The resulting high-density genetic map contained 782 single-nucleotide polymorphisms (SNPs) and spanned a length of 697.3 cM, with an average marker interval of 0.89 cM. Based on the reference genome, the capsule shattering trait was mapped onto SNP marker S8_5062843 (78.9 cM) near the distal end of LG8 (chromosome 8). In order to reveal genes potentially controlling the shattering trait, the marker region (S8_5062843) was examined, and a candidate gene including six CDSs was identified. Annotation showed that the gene encodes a protein with 440 amino acids, sharing ∼99% homology with transcription repressor KAN1. Compared with the capsule shattering allele, the SNP change and altered splicing in the flanking region of S8_5062843 caused a frameshift mutation in the mRNA, resulting in the loss of function of this gene in the mutant parent and thus in non-shattering capsules and leaf curling. With the use of genomic data, InDel and CAPS markers were developed to differentiate shattering and non-shattering capsule genotypes in marker-assisted selection studies. The obtained results in the study can be beneficial in breeding programs to improve the shattering trait and enhance sesame productivity.

scholarly journals Frequent gain- and loss-of-function mutations of the BjMYB113 gene accounted for leaf color variation in Brassica juncea

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Guanghui An ◽  
Jiongjiong Chen
Keyword(s):  
Brassica Juncea ◽  
Anthocyanin Biosynthesis ◽  
Color Variation ◽  
Nucleotide Polymorphisms ◽  
Loss Of Function ◽  
High Accumulation ◽  
Single Nucleotide ◽  
Breeding Programs ◽  
Promoter Sequences ◽  
Expression Of Genes

Abstract Background Mustard (Brassica juncea) is an important economic vegetable, and some cultivars have purple leaves and accumulate more anthocyanins than the green. The genetic and evolution of purple trait in mustard has not been well studied. Result In this study, free-hand sections and metabolomics showed that the purple leaves of mustard accumulated more anthocyanins than green ones. The gene controlling purple leaves in mustard, Mustard Purple Leaves (MPL), was genetically mapped and a MYB113-like homolog was identified as the candidate gene. We identified three alleles of the MYB113-like gene, BjMYB113a from a purple cultivar, BjMYB113b and BjMYB113c from green cultivars. A total of 45 single nucleotide polymorphisms (SNPs) and 8 InDels were found between the promoter sequences of the purple allele BjMYB113a and the green allele BjMYB113b. On the other hand, the only sequence variation between the purple allele BjMYB113a and the green allele BjMYB113c is an insertion of 1,033-bp fragment in the 3’region of BjMYB113c. Transgenic assay and promoter activity studies showed that the polymorphism in the promoter region was responsible for the up-regulation of the purple allele BjMYB113a and high accumulation of anthocyanin in the purple cultivar. The up-regulation of BjMYB113a increased the expression of genes in the anthocyanin biosynthesis pathway including BjCHS, BjF3H, BjF3’H, BjDFR, BjANS and BjUGFT, and consequently led to high accumulation of anthocyanin. However, the up-regulation of BjMYB113 was compromised by the insertion of 1,033-bp in 3’region of the allele BjMYB113c. Conclusions Our results contribute to a better understanding of the genetics and evolution of the BjMYB113 gene controlling purple leaves and provide useful information for further breeding programs of mustard.

RAD-seq-Based High-Density Linkage Map Construction and QTL Mapping of Biomass-Related Traits in Sorghum using the Japanese Landrace Takakibi NOG

2020 ◽  
Vol 61 (7) ◽  
pp. 1262-1272
Author(s):  
Hiromi Kajiya-Kanegae ◽  
Hideki Takanashi ◽  
Masaru Fujimoto ◽  
Motoyuki Ishimori ◽  
Norikazu Ohnishi ◽  
...  
Keyword(s):  
Linkage Map ◽  
High Density ◽  
Genomic Diversity ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Genetic Traits ◽  
Map Construction ◽  
Days To Heading ◽  
High Density Linkage Map ◽  
Sorghum Bicolor L

Abstract Sorghum [Sorghum bicolor (L.) Moench] grown locally by Japanese farmers is generically termed Takakibi, although its genetic diversity compared with geographically distant varieties or even within Takakibi lines remains unclear. To explore the genomic diversity and genetic traits controlling biomass and other physiological traits in Takakibi, we focused on a landrace, NOG, in this study. Admixture analysis of 460 sorghum accessions revealed that NOG belonged to the subgroup that represented Asian sorghums, and it was only distantly related to American/African accessions including BTx623. In an attempt to dissect major traits related to biomass, we generated a recombinant inbred line (RIL) from a cross between BTx623 and NOG, and we constructed a high-density linkage map based on 3,710 single-nucleotide polymorphisms obtained by restriction-site-associated DNA sequencing of 213 RIL individuals. Consequently, 13 fine quantitative trait loci (QTLs) were detected on chromosomes 2, 3, 6, 7, 8 and 9, which included five QTLs for days to heading, three for plant height (PH) and total shoot fresh weight and two for Brix. Furthermore, we identified two dominant loci for PH as being identical to the previously reported dw1 and dw3. Together, these results corroborate the diversified genome of Japanese Takakibi, while the RIL population and high-density linkage map generated in this study will be useful for dissecting other important traits in sorghum.

Frequent Gain- and Loss-of-Function Mutations of the BjMYB113 Gene Accounted for Leaf Color Variation in Brassica Juncea

2021 ◽  
Author(s):  
Guanghui An ◽  
Jiongjiong Chen
Keyword(s):  
Brassica Juncea ◽  
Anthocyanin Biosynthesis ◽  
Color Variation ◽  
Nucleotide Polymorphisms ◽  
Loss Of Function ◽  
High Accumulation ◽  
Single Nucleotide ◽  
Breeding Programs ◽  
Promoter Sequences ◽  
Expression Of Genes

Abstract Background: Mustard (Brassica juncea) is an important vegetable, and some cultivars have purple leaves and accumulate more anthocyanins than the green. The genetic and evolution of purple trait in mustard has not been well studied. Result: In this study, free-hand sections and metabolomics showed that the purple leaves of mustard accumulated more anthocyanins than green ones. The trait of purple leaves in mustard, Mustard Purple Leaves (MPL), was genetically mapped and a MYB113-like homolog was identified as the candidate gene. We identified three alleles of the MYB113-like gene, BjMYB113a from a purple cultivar, BjMYB113b and BjMYB113c from green cultivars. A total of 45 single nucleotide polymorphisms (SNPs) and 8 InDels were found between the promoter sequences of the purple allele BjMYB113a and the green allele BjMYB113b. On the other hand, the only sequence variation between the purple allele BjMYB113a and the green allele BjMYB113c is an insertion of 1,033-bp fragment in the 3’region of BjMYB113c. Transgenic assay and promoter activity studies showed that the polymorphism in the promoter region was responsible for the up-regulation of the purple allele BjMYB113a and high accumulation of anthocyanin in the purple cultivar. The up-regulation of BjMYB113a increased the expression of genes in the anthocyanin biosynthesis pathway including BjCHS, BjF3H, BjF3’H, BjDFR, BjANS and BjUGFT, and consequently led to high accumulation of anthocyanin. However, the up-regulation of BjMYB113 was compromised by the insertion of 1,033-bp in 3’region of the allele BjMYB113c. Conclusion: Our results contribute to a better understanding of the genetics and evolution of the BjMYB113 gene controlling purple leaves and provide useful information for further breeding programs of mustard.

scholarly journals Genotyping-by-Sequencing of Gossypium hirsutum Races and Cultivars Uncovers Novel Patterns of Genetic Relationships and Domestication Footprints

2019 ◽  
Vol 15 ◽  
pp. 117693431988994
Author(s):  
Shulin Zhang ◽  
Yaling Cai ◽  
Jinggong Guo ◽  
Kun Li ◽  
Renhai Peng ◽  
...  
Keyword(s):  
Gossypium Hirsutum ◽  
Genetic Relationships ◽  
Phylogenetic Analyses ◽  
Genotyping By Sequencing ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Breeding Programs ◽  
Association Analyses ◽  
Genome Wide ◽  
Candidate Gene Locus

Determining the genetic rearrangement and domestication footprints in Gossypium hirsutum cultivars and primitive race genotypes are essential for effective gene conservation efforts and the development of advanced breeding molecular markers for marker-assisted breeding. In this study, 94 accessions representing the 7 primitive races of G hirsutum, along with 9 G hirsutum and 12 Gossypium barbadense cultivated accessions were evaluated. The genotyping-by-sequencing (GBS) approach was employed and 146 558 single nucleotide polymorphisms (SNP) were generated. Distinct SNP signatures were identified through the combination of selection scans and association analyses. Phylogenetic analyses were also conducted, and we concluded that the Latifolium, Richmondi, and Marie-Galante race accessions were more genetically related to the G hirsutum cultivars and tend to cluster together. Fifty-four outlier SNP loci were identified by selection-scan analysis, and 3 SNPs were located in genes related to the processes of plant responding to stress conditions and confirmed through further genome-wide signals of marker-phenotype association analysis, which indicate a clear selection signature for such trait. These results identified useful candidate gene locus for cotton breeding programs.

scholarly journals Investigation of Genetic Relationships within Miscanthus using SNP Markers Identified using SLAF-Seq

2021 ◽  
Author(s):  
ZHIYONG Chen ◽  
Yancen He ◽  
Yasir Iqbal ◽  
Yanlan Shi ◽  
Hongmei Huang ◽  
...  
Keyword(s):  
High Throughput ◽  
High Throughput Sequencing ◽  
Genetic Relationships ◽  
Female Parent ◽  
Snp Markers ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Breeding Programs ◽  
Sequencing Method ◽  
Specific Locus

Abstract Background: Miscanthus, which is a leading dedicated-energy grass in Europe and in parts of Asia, is expected to play a key role in the development of the future bioeconomy. However, due to its complex genetic background, it is difficult to investigate phylogenetic relationships and the evolution of gene function in this genus. Here, we investigated 50 Miscanthus germplasms: 1 female parent (M. lutarioriparius), 30 candidate male parents (M. lutarioriparius, M. sinensis, and M. sacchariflorus), and 19 offspring. We used high-throughput Specific-Locus Amplified Fragment sequencing (SLAF-seq) to identify informative single nucleotide polymorphisms (SNPs) in all germplasms.Results: We identified 800,081 SLAF tags, of which 160,368 were polymorphic. Each tag was 264–364 bp long. The obtained SNPs were used to investigate genetic relationships within Miscanthus. We constructed a phylogenetic tree of the 50 germplasms using the obtained SNPs, and found that the germplasms fell into two clades: one clade of M. sinensis only and one clade that included the offspring, M. lutarioriparius, and M. sacchariflorus. Genetic cluster analysis indicated that M. lutarioriparius germplasm C3 was the most likely male parent of the offspring.Conclusions: As a high-throughput sequencing method, SLAF-seq can be used to identify informative SNPs in Miscanthus germplasms and to rapidly characterize genetic relationships within this genus. Our results will support the development of breeding programs utilizing Miscanthus cultivars with elite biomass- or fiber-production potential.

Two Novel Polymorphisms in 5' Flanking Region of the Mesothelin Gene are Associated with Soluble Mesothelin-Related Peptide (SMRP) Levels

2011 ◽  
Vol 26 (2) ◽  
pp. 117-123 ◽  
Author(s):  
Alfonso Cristaudo ◽  
Rudy Foddis ◽  
Alessandra Bonotti ◽  
Silvia Simonini ◽  
Agnese Vivaldi ◽  
...  
Keyword(s):  
Healthy Subjects ◽  
Fold Increase ◽  
High Rate ◽  
Pleural Mesothelioma ◽  
Clinical Use ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Elisa Kit ◽  
Surveillance Programs ◽  
Flanking Region

Background and aims Increased concentrations of soluble mesothelin-related peptides (SMRP) have been found in sera of patients with malignant pleural mesothelioma (MPM) even if a relatively high rate of false positives has hampered their clinical use as a tumor marker. Individual SMRP levels could be affected by polymorphic elements. The aim of this study was to investigate the association between single nucleotide polymorphisms within the promoter-5'UTR regions and SMRP levels in healthy asbestos-exposed individuals and patients suffering from MPM. Methods The promoter-5'UTR regions of the mesothelin gene were genotyped in 59 healthy asbestos-exposed subjects and 27 MPM patients. SMRP levels were measured using a commercially available ELISA kit. Results Two novel polymorphisms, an A>C variant (called New1) and a C>T variant (called New2), were identified. In healthy subjects, high SMRP levels were associated with the C-variant of New1, with an average 1.62-fold increase compared with AA homozygotes (p<0.0001). Most of the C-allele carriers had SMRP levels above the threshold of 1.00 nM. We set two different SMRP cutoffs on the basis of the combined New1+New2 genotypes. Conclusions New1-New2 genotypes could be employed as markers for setting individualized and appropriate thresholds of “normality” when SMRP is used in surveillance programs of asbestos-exposed people.

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