scholarly journals Identification and Characterization of DAMs Mutations Associated With Early Blooming in Sweet Cherry, and Validation of DNA-Based Markers for Selection

2021 ◽  
Vol 12 ◽  
Author(s):  
Alejandro Calle ◽  
Jérôme Grimplet ◽  
Loïck Le Dantec ◽  
Ana Wünsch
Keyword(s):  
Amino Acid ◽  
Candidate Genes ◽  
Sweet Cherry ◽  
Genomic Structure ◽  
Chromosome 1 ◽  
Change Scenario ◽  
Pcr Markers ◽  
Japanese Apricot ◽  
Amino Acid Variability ◽  
Structural Mutations

Dormancy release and bloom time of sweet cherry cultivars depend on the environment and the genotype. The knowledge of these traits is essential for cultivar adaptation to different growing areas, and to ensure fruit set in the current climate change scenario. In this work, the major sweet cherry bloom time QTL qP-BT1.1m (327 Kbs; Chromosome 1) was scanned for candidate genes in the Regina cv genome. Six MADS-box genes (PavDAMs), orthologs to peach and Japanese apricot DAMs, were identified as candidate genes for bloom time regulation. The complete curated genomic structure annotation of these genes is reported. To characterize PavDAMs intra-specific variation, genome sequences of cultivars with contrasting chilling requirements and bloom times (N = 13), were then mapped to the ‘Regina’ genome. A high protein sequence conservation (98.8–100%) was observed. A higher amino acid variability and several structural mutations were identified in the low-chilling and extra-early blooming cv Cristobalina. Specifically, a large deletion (694 bp) upstream of PavDAM1, and various INDELs and SNPs in contiguous PavDAM4 and -5 UTRs were identified. PavDAM1 upstream deletion in ‘Cristobalina’ revealed the absence of several cis-acting motifs, potentially involved in PavDAMs expression. Also, due to this deletion, a non-coding gene expressed in late-blooming ‘Regina’ seems truncated in ‘Cristobalina’. Additionally, PavDAM4 and -5 UTRs mutations revealed different splicing variants between ‘Regina’ and ‘Cristobalina’ PavDAM5. The results indicate that the regulation of PavDAMs expression and post-transcriptional regulation in ‘Cristobalina’ may be altered due to structural mutations in regulatory regions. Previous transcriptomic studies show differential expression of PavDAM genes during dormancy in this cultivar. The results indicate that ‘Cristobalina’ show significant amino acid differences, and structural mutations in PavDAMs, that correlate with low-chilling and early blooming, but the direct implication of these mutations remains to be determined. To complete the work, PCR markers designed for the detection of ‘Cristobalina’ structural mutations in PavDAMs, were validated in an F2 population and a set of cultivars. These PCR markers are useful for marker-assisted selection of early blooming seedlings, and probably low-chilling, from ‘Cristobalina’, which is a unique breeding source for these traits.

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.

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.

AFX1 and p54 nrb : fine mapping, genomic structure, and exclusion as candidate genes of X-linked dystonia parkinsonism

1997 ◽  
Vol 100 (5-6) ◽  
pp. 569-572 ◽  
Author(s):  
Usha Peters ◽  
Gerd Haberhausen ◽  
Markus Kostrzewa ◽  
Dagmar Nolte ◽  
U. Müller
Keyword(s):  
Candidate Genes ◽  
Fine Mapping ◽  
Genomic Structure

Biochemical data bearing on the origin of the B genome in the polyploid wheats

Genome ◽  
1990 ◽  
Vol 33 (3) ◽  
pp. 360-368 ◽  
Author(s):  
K. Kerby ◽  
J. Kuspira ◽  
B. L. Jones ◽  
G. L. Lookhart
Keyword(s):  
Amino Acid ◽  
B Chromosome ◽  
Amino Acid Sequences ◽  
Chromosome 1 ◽  
Aegilops Speltoides ◽  
B Genome ◽  
Aegilops Longissima ◽  
Aegilops Sharonensis ◽  
A Genome ◽  
Genome Donors

For many years each of the species Aegilops bicornis, Aegilops longissima, Aegilops searsii, Aegilops sharonensis, Aegilops speltoides, and Triticum urartu has been implicated as the donor of the B genome in the polyploid wheats. Biochemical and cytological data have revealed that T. urartu possesses a genome similar to that of T. monococcum, and therefore it may be the source of the A genome in T. turgidum and T. aestivum. This revelation therefore excludes T. urartu from the list of putative B-genome donors. To determine which of the remaining species is the source of the B chromosome set, the amino acid sequences of their purothionins were compared with that of the α1 purothionin coded for by the Pur-1B gene on chromosome 1 in the B genome of T. turgidum and T. aestivum. The residue sequences of this protein from Ae. bicornis, Ae. longissima, Ae. searsii, Ae. sharonensis, and Ae. speltoides differed by 1, 6, 1, 1, and 2 amino acid substitutions, respectively, from the α1 protein. These results suggest that either Ae. bicornis, Ae. searsii, or Ae. sharonensis was the most likely donor of the B genome. If the B genome in the polyploid wheats is monophyletic in origin, the collective findings of this and other investigations indicate that Ae. searsii is the most likely donor. The possibility that the B genome in the polyploid wheats could have a polyphyletic origin is also discussed.Key words: polyploid wheats, putative B-genome donors, purothionins, monophyletic, polyphyletic.

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

scholarly journals Identification of candidate genes that underlie the QTL on chromosome 1 that mediates genetic differences in stress-ethanol interactions

2015 ◽  
Vol 47 (8) ◽  
pp. 308-317 ◽  
Author(s):  
Melloni N. Cook ◽  
Jessica A. Baker ◽  
Scott A. Heldt ◽  
Robert W. Williams ◽  
Kristin M. Hamre ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Genome Wide Association Study ◽  
Zinc Finger Protein ◽  
Genetic Differences ◽  
Chromosome 1 ◽  
Protein Tyrosine ◽  
Finger Protein ◽  
Genome Wide ◽  
Trait Locus ◽  
Tyrosine Phosphate

Alcoholism, stress, and anxiety are strongly interacting heritable, polygenetic traits. In a previous study, we identified a quantitative trait locus (QTL) on murine chromosome (Chr) 1 between 23.0 and 31.5 Mb that modulates genetic differences in the effects of ethanol on anxiety-related phenotypes. The goal of the present study was to extend the analysis of this locus with a focus on identifying candidate genes using newly available data and tools. Anxiety-like behavior was evaluated with an elevated zero maze following saline or ethanol injections (1.8 g/kg) in C57BL/6J, DBA2J, and 72 BXD strains. We detected significant effects of strain and treatment and their interaction on anxiety-related behaviors, although surprisingly, sex was not a significant factor. The Chr1 QTL is specific to the ethanol-treated cohort. Candidate genes in this locus were evaluated using now standard bioinformatic criteria. Collagen 19a1 ( Col19a1) and family sequence 135a ( Fam135a) met most criteria but have lower expression levels and lacked biological verification and, therefore, were considered less likely candidates. In contrast, two other genes, the prenylated protein tyrosine phosphate family member Ptp4a1 (protein tyrosine phosphate 4a1) and the zinc finger protein Phf3 (plant homeoDomain finger protein 3) met each of our bioinformatic criteria and are thus strong candidates. These findings are also of translational relevance because both Ptp4a1 and Phf3 have been nominated as candidates genes for alcohol dependence in a human genome-wide association study. Our findings support the hypothesis that variants in one or both of these genes modulate heritable differences in the effects of ethanol on anxiety-related behaviors.

scholarly journals Mapping quantitative trait loci and predicting candidate genes for leaf angle in maize

PLoS ONE ◽  
2021 ◽  
Vol 16 (1) ◽  
pp. e0245129
Author(s):  
Ning Zhang ◽  
Xueqing Huang
Keyword(s):  
Candidate Genes ◽  
Inbred Line ◽  
Plant Architecture ◽  
Crop Yields ◽  
Recombinant Inbred Lines ◽  
Chromosome 1 ◽  
Leaf Angle ◽  
Compact Leaf ◽  
Leaf Architecture ◽  
Maize Varieties

Leaf angle of maize is a fundamental determinant of plant architecture and an important trait influencing photosynthetic efficiency and crop yields. To broaden our understanding of the genetic mechanisms of leaf angle formation, we constructed a F3:4 recombinant inbred lines (RIL) population to map QTL for leaf angle. The RIL was derived from a cross between a model inbred line (B73) with expanded leaf architecture and an elite inbred line (Zheng58) with compact leaf architecture. A sum of eight QTL were detected on chromosome 1, 2, 3, 4 and 8. Single QTL explained 4.3 to 14.2% of the leaf angle variance. Additionally, some important QTL were confirmed through a heterogeneous inbred family (HIF) approach. Furthermore, twenty-four candidate genes for leaf angle were predicted through whole-genome re-sequencing and expression analysis in qLA02-01and qLA08-01 regions. These results will be helpful to elucidate the genetic mechanism of leaf angle formation in maize and benefit to clone the favorable allele for leaf angle. Besides, this will be helpful to develop the novel maize varieties with ideal plant architecture through marker-assisted selection.

Sign in / Sign up

Export Citation Format

Share Document