scholarly journals Newly developed MAGIC population allows identification of strong associations and candidate genes for anthocyanin pigmentation in eggplant

2021 ◽  
Author(s):  
Giulio Mangino ◽  
Andrea Arrones ◽  
Mariola Plazas ◽  
Torsten Pook ◽  
Jaime Prohens ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Anthocyanin Biosynthesis ◽  
Regulatory Protein ◽  
Solanum Melongena ◽  
Nuclear Genome ◽  
Chromosome 1 ◽  
Genetic Dissection ◽  
Myb Genes ◽  
Recombinant Population ◽  
Magic Population

SummaryMAGIC populations facilitate the genetic dissection of complex quantitative traits in plants and are valuable breeding materials. We report the development of the first eggplant MAGIC population (S3MEGGIC; 8-way), constituted by 420 S3 individuals developed from the intercrossing of seven cultivated eggplant (Solanum melongena) and one wild relative (S. incanum) parents. The S3MEGGIC recombinant population was genotyped with the eggplant 5k probes SPET platform and phenotyped for anthocyanins presence in vegetative plant tissues (PA) and fruit epidermis (FA), and for the light-sensitive anthocyanic pigmentation under the calyx (PUC). The 7,724 filtered high-confidence SNPs confirmed a low residual heterozygosity (6.87%) and a lack of genetic structure in the S3MEGGIC population, including no differentiation among subpopulations carrying cultivated or wild cytoplasm. Inference of haplotype blocks of the nuclear genome revealed an unbalanced representation of founder genomes, suggesting cryptic selection in favour or against specific parental genomes. GWAS analysis for PA, FA and PUC detected strong associations with two MYB genes similar to MYB113 involved in the anthocyanin biosynthesis pathway and with a COP1 gene, which encodes for a photo-regulatory protein and may be responsible for the PUC phenotype. Evidence was found of a duplication of an ancestral MYB113 gene with a translocation from chromosome 10 to chromosome 1. Parental genotypes for the three genes were in agreement with the candidate genes identification performed in the S3MEGGIC population. Our new eggplant MAGIC population is the largest recombinant population in eggplant and is a powerful tool for eggplant genetics and breeding studies.

scholarly journals Identification of Candidate Gene for Internode Length in Rice to Enhance Resistance to Lodging Using QTL Analysis

Plants ◽  
2021 ◽  
Vol 10 (7) ◽  
pp. 1369
Author(s):  
Dan-Dan Zhao ◽  
Ju-Hyeong Son ◽  
Muhammad Farooq ◽  
Kyung-Min Kim
Keyword(s):  
Candidate Genes ◽  
Qtl Analysis ◽  
Middle Part ◽  
Internode Length ◽  
Stem Diameter ◽  
Chromosome 1 ◽  
Doubled Haploid Population ◽  
Lodging Resistance ◽  
Cytochrome P450 Family ◽  
Uppermost Internode

Internode length and stem diameter are the primary traits affecting the lodging resistance of rice. Traits related to the length of the panicle (LP), uppermost internode (LUI), second internode (LSI), third internode (LTI), fourth internode (LFI), lowest internode (LLI) as well as stem diameter at the uppermost internode (SDUI), second internode (SDSI), third internode (SDTI), fourth internode (SDFI), and lowest internode (SDLI) in 120 Cheongcheong/Nagdong doubled haploid population were investigated using a quantitative trait locus (QTL) analysis. Thirty-four QTL regions affected LP and the length of each internode. Twenty-six QTL regions were associated with the stem diameter of each internode. RM12285-RM212 on chromosome 1 contained 10 QTLs related to the internode length, which have overlapped for over 2 years. Twenty-three candidate genes were screened using mark interval. Among the candidate genes, Os01g0803900, named OsCYPq1, which is in the Cytochrome P450 family, might be involved in gibberellins (GA) synthesis. GA is an essential plant growth regulator that affects plant height. OsCYPq1 catalyzes oxidation steps in the middle part of the GA pathway. OsCYPq1 is expected to provide valuable information to improve the marker assessment for target traits and QTL gene cloning in rice.

CBFs Function in Anthocyanin Biosynthesis by Interacting with MYB113 in Eggplant (Solanum melongena L.)

2019 ◽  
Vol 61 (2) ◽  
pp. 416-426 ◽  
Author(s):  
Lu Zhou ◽  
Yongjun He ◽  
Jing Li ◽  
Yang Liu ◽  
Huoying Chen
Keyword(s):  
Low Temperature ◽  
Anthocyanin Biosynthesis ◽  
Solanum Melongena ◽  
Structural Genes ◽  
Cold Response ◽  
Anthocyanin Pathway ◽  
R2r3 Myb ◽  
Dependent Pathway ◽  
Shed Light ◽  
R2r3 Myb Transcription Factors

Abstract Eggplant is rich in anthocyanins. R2R3-MYB transcription factors play a key role in the anthocyanin pathway. Low temperature is vital abiotic stress that affects the anthocyanin biosynthesis in plants. CBFs (C-repeat binding factors) act as central regulators in cold response. In this study, we found that SmCBF1, SmCBF2 and SmCBF3, via their C-terminal, physically interacted with SmMYB113, a key regulator of anthocyanin biosynthesis in eggplant. SmCBF2 and SmCBF3 upregulated the expression of SmCHS and SmDFR via a SmMYB113-dependent pathway. In addition, the transient expression assays demonstrated that co-infiltrating SmCBFs and SmMYB113 significantly improved the contents of anthocyanin and the expression levels of anthocyanin structural genes in tobacco. When SmTT8, a bHLH partner of SmMYB113, coexpressed with SmCBFs and SmMYB113, the anthocyanin contents were significantly enhanced compared with SmCBFs and SmMYB113. Furthermore, overexpression of SmCBF2 and SmCBF3 could facilitate the anthocyanin accumulation under cold conditions in Arabidopsis. Taken together, these results shed light on the functions of SmCBFs and potential mechanisms of low-temperature-induced anthocyanin biosynthesis in eggplant.

scholarly journals Red Chinese Cabbage Transcriptome Analysis Reveals Structural Genes and Multiple Transcription Factors Regulating Reddish Purple Color

2020 ◽  
Vol 21 (8) ◽  
pp. 2901 ◽  
Author(s):  
Jana Jeevan Rameneni ◽  
Su Ryun Choi ◽  
Sushil Satish Chhapekar ◽  
Man-Sun Kim ◽  
Sonam Singh ◽  
...  
Keyword(s):  
Chinese Cabbage ◽  
Anthocyanin Biosynthesis ◽  
Gene Promoters ◽  
Biosynthesis Pathway ◽  
Transcriptome Data ◽  
Biosynthetic Gene ◽  
Structural Genes ◽  
Regulatory Motifs ◽  
Myb Genes ◽  
Anthocyanin Biosynthetic Genes

Reddish purple Chinese cabbage (RPCC) is a popular variety of Brassica rapa (AA = 20). It is rich in anthocyanins, which have many health benefits. We detected novel anthocyanins including cyanidin 3-(feruloyl) diglucoside-5-(malonoyl) glucoside and pelargonidin 3-(caffeoyl) diglucoside-5-(malonoyl) glucoside in RPCC. Analyses of transcriptome data revealed 32,395 genes including 3345 differentially expressed genes (DEGs) between 3-week-old RPCC and green Chinese cabbage (GCC). The DEGs included 218 transcription factor (TF) genes and some functionally uncharacterized genes. Sixty DEGs identified from the transcriptome data were analyzed in 3-, 6- and 9-week old seedlings by RT-qPCR, and 35 of them had higher transcript levels in RPCC than in GCC. We detected cis-regulatory motifs of MYB, bHLH, WRKY, bZIP and AP2/ERF TFs in anthocyanin biosynthetic gene promoters. A network analysis revealed that MYB75, MYB90, and MYBL2 strongly interact with anthocyanin biosynthetic genes. Our results show that the late biosynthesis genes BrDFR, BrLDOX, BrUF3GT, BrUGT75c1-1, Br5MAT, BrAT-1, BrAT-2, BrTT19-1, and BrTT19-2 and the regulatory MYB genes BrMYB90, BrMYB75, and BrMYBL2-1 are highly expressed in RPCC, indicative of their important roles in anthocyanin biosynthesis, modification, and accumulation. Finally, we propose a model anthocyanin biosynthesis pathway that includes the unique anthocyanin pigments and genes specific to RPCC.

scholarly journals Nested‐association mapping (NAM)‐based genetic dissection uncovers candidate genes for seed and pod weights in peanut ( Arachis hypogaea )

2019 ◽  
Vol 18 (6) ◽  
pp. 1457-1471
Author(s):  
Sunil S. Gangurde ◽  
Hui Wang ◽  
Shasidhar Yaduru ◽  
Manish K. Pandey ◽  
Jake C. Fountain ◽  
...  
Keyword(s):  
Association Mapping ◽  
Candidate Genes ◽  
Arachis Hypogaea ◽  
Genetic Dissection ◽  
Nested Association Mapping

scholarly journals Genetic dissection of canine hip dysplasia phenotypes and osteoarthritis reveals three novel loci

BMC Genomics ◽  
2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Lea Mikkola ◽  
Saila Holopainen ◽  
Tiina Pessa-Morikawa ◽  
Anu K. Lappalainen ◽  
Marjo K. Hytönen ◽  
...  
Keyword(s):  
Hip Dysplasia ◽  
Cartilage Degradation ◽  
Chromosome 9 ◽  
Chromosome 1 ◽  
Severe Dysplasia ◽  
Genetic Dissection ◽  
Genes Encoding ◽  
Joint Incongruity ◽  
Canine Hip Dysplasia ◽  
Norberg Angle

Abstract Background Hip dysplasia and osteoarthritis continue to be prevalent problems in veterinary and human medicine. Canine hip dysplasia is particularly problematic as it massively affects several large-sized breeds and can cause a severe impairment of the quality of life. In Finland, the complex condition is categorized to five classes from normal to severe dysplasia, but the categorization includes several sub-traits: congruity of the joint, Norberg angle, subluxation degree of the joint, shape and depth of the acetabulum, and osteoarthritis. Hip dysplasia and osteoarthritis have been proposed to have separate genetic etiologies. Results Using Fédération Cynologique Internationale -standardized ventrodorsal radiographs, German shepherds were rigorously phenotyped for osteoarthritis, and for joint incongruity by Norberg angle and femoral head center position in relation to dorsal acetabular edge. The affected dogs were categorized into mild, moderate and severe dysplastic phenotypes using official hip scores. Three different genome-wide significant loci were uncovered. The strongest candidate genes for hip joint incongruity were noggin (NOG), a bone and joint developmental gene on chromosome 9, and nanos C2HC-type zinc finger 1 (NANOS1), a regulator of matrix metalloproteinase 14 (MMP14) on chromosome 28. Osteoarthritis mapped to a long intergenic region on chromosome 1, between genes encoding for NADPH oxidase 3 (NOX3), an intriguing candidate for articular cartilage degradation, and AT-rich interactive domain 1B (ARID1B) that has been previously linked to joint laxity. Conclusions Our findings highlight the complexity of canine hip dysplasia phenotypes. In particular, the results of this study point to the potential involvement of specific and partially distinct loci and genes or pathways in the development of incongruity, mild dysplasia, moderate-to-severe dysplasia and osteoarthritis of canine hip joints. Further studies should unravel the unique and common mechanisms for the various sub-traits.

Genome-wide association study provides insights into the genetic architecture of bone size and mass in chickens

Genome ◽  
2020 ◽  
Vol 63 (3) ◽  
pp. 133-143 ◽  
Author(s):  
Jun Guo ◽  
Liang Qu ◽  
Tao-Cun Dou ◽  
Man-Man Shen ◽  
Yu-Ping Hu ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Linear Mixed Model ◽  
Bone Size ◽  
Chromosome 1 ◽  
Meat Production ◽  
Phenotypic Variance ◽  
Femur Length ◽  
Genome Wide ◽  
Length And Area ◽  
Tibia Length

Bone size is an important trait for chickens because of its association with osteoporosis in layers and meat production in broilers. Here, we employed high density genotyping platforms to detect candidate genes for bone traits. Estimates of the narrow heritabilities ranged from 0.37 ± 0.04 for shank length to 0.59 ± 0.04 for tibia length. The dominance heritability was 0.12 ± 0.04 for shank length. Using a linear mixed model approach, we identified a promising locus within NCAPG on chromosome 4, which was associated with tibia length and mass, femur length and area, and shank length. In addition, three other loci were associated with bone size or mass at a Bonferroni-corrected genome-wide significance threshold of 1%. One region on chicken chromosome 1 between 168.38 and 171.82 Mb harbored HTR2A, LPAR6, CAB39L, and TRPC4. A second region that accounted for 2.2% of the phenotypic variance was located around WNT9A on chromosome 2, where allele substitution was predicted to be associated with tibia length. Four candidate genes identified on chromosome 27 comprising SPOP, NGFR, GIP, and HOXB3 were associated with tibia length and mass, femur length and area, and shank length. Genome partitioning analysis indicated that the variance explained by each chromosome was proportional to its length.

scholarly journals Genetic profiling of chromosome 1 in breast cancer: mapping of regions of gains and losses and identification of candidate genes on 1q

2006 ◽  
Vol 95 (10) ◽  
pp. 1439-1447 ◽  
Author(s):  
B Orsetti ◽  
M Nugoli ◽  
N Cervera ◽  
L Lasorsa ◽  
P Chuchana ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Candidate Genes ◽  
Chromosome 1 ◽  
Genetic Profiling ◽  
Gains And Losses
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