Dissection of a major QTL for seed colour and fibre content inBrassica napusreveals colocalization with candidate genes for phenylpropanoid biosynthesis and flavonoid deposition

2013 ◽  
Vol 132 (4) ◽  
pp. 382-389 ◽  
Author(s):  
Anna Stein ◽  
Benjamin Wittkop ◽  
Liezhao Liu ◽  
Christian Obermeier ◽  
Wolfgang Friedt ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Fibre Content ◽  
Seed Colour ◽  
Phenylpropanoid Biosynthesis ◽  
Major Qtl

Colocalization of a partially dominant gene for yellow seed colour with a major QTL influencing acid detergent fibre (ADF) content in different crosses of oilseed rape (Brassica napus)

Genome ◽  
2006 ◽  
Vol 49 (12) ◽  
pp. 1499-1509 ◽  
Author(s):  
Ana Gloria Badani ◽  
Rod J. Snowdon ◽  
Benjamin Wittkop ◽  
Florin D. Lipsa ◽  
Roland Baetzel ◽  
...  
Keyword(s):  
Brassica Napus ◽  
Oilseed Rape ◽  
Dominant Gene ◽  
Fibre Content ◽  
Clear Correlation ◽  
Potential Candidate ◽  
Seed Colour ◽  
Yellow Seed ◽  
Acid Detergent Fibre ◽  
Major Qtl

Quantitative trait loci (QTLs) contributing to yellow seed colour and acid detergent fibre (ADF) were localized and compared in 3 mapping populations developed from 2 crosses (designated ‘YE1’ and ‘YE2’) between 2 distinct sources of true-breeding yellow-seeded oilseed rape (Brassica napus) and 2 different black-seeded genotypes. A clear correlation was observed between seed colour and ADF content in both crosses. In all 3 populations, a major QTL, with a large effect on both seed colour and ADF in multiple environments, was detected at the same position on chromosome N18. In YE1, a second minor QTL, with a small effect on seed colour but not on ADF content, was localized on chromosome N1. In YE2, no QTL was observed on N1; however, 2 minor seed-colour loci were localized to N15 and N5. A second major QTL for ADF was localized in YE1 on N13; in YE2, no other QTLs for ADF were detected. Combined QTL and segregation data for seed colour and ADF content in the different populations suggest that a partially dominant B. napus gene for seed colour on N18 contributes to a reduction in fibre content in different yellow-seeded B. napus genotypes. The other QTLs that were identified appear to represent different genes in the 2 yellow-seeded rapeseed sources, which, in each case, affect only fibre content or seed colour, respectively. Potential candidate genes and implications for marker-assisted breeding of oilseed rape with reduced seed dietary fibre content are discussed.

A major QTL and candidate genes for capsaicinoid biosynthesis in the pericarp of Capsicum chinense revealed using QTL-seq and RNA-seq

2018 ◽  
Vol 132 (2) ◽  
pp. 515-529 ◽  
Author(s):  
Minjeong Park ◽  
Joung-Ho Lee ◽  
Koeun Han ◽  
Siyoung Jang ◽  
Jiwoong Han ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Rna Seq ◽  
Capsicum Chinense ◽  
Major Qtl ◽  
Capsaicinoid Biosynthesis

scholarly journals Identification and fine mapping of qPBR10-1, a novel locus controlling panicle blast resistance in Pigm-containing P/TGMS line

2021 ◽  
Author(s):  
Yunyu Wu ◽  
Ning Xiao ◽  
Yuhong Li ◽  
Qiang Gao ◽  
Yuese Ning ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Sequence Comparison ◽  
Blast Resistance ◽  
Rt Pcr ◽  
Advanced Backcross ◽  
Family Protein ◽  
Panicle Blast ◽  
Genes Encoding ◽  
Causal Candidate ◽  
Major Qtl

Abstract Background Rice blast is one of the most widespread and devastating diseases in rice production. Tremendous success has been achieved in identification and characterization of genes and quantitative trait loci (QTLs) conferring seedling blast resistance, however, genetic studies on panicle blast resistance have lagged far behind. Results In this study, two advanced backcross inbred sister lines (MSJ13 and MSJ18) were obtained in the process of introducing Pigm into C134S, and showed significant differences in the panicle blast resistance. One F2 population derived from the crossing MSJ13/MSJ18 was used to QTL mapping for panicle blast resistance using Genotyping by Sequencing (GBS) method. A total of 7 QTLs were identified, including a major QTL qPBR10-1 on chromosome 10 that explaining 24.21% of phenotypic variance with LOD scores of 6.62. Furthermore, qPBR10-1 was verified via the BC1F2 and BC1F3 population and narrowed to a 60.6-kb region with six candidate genes predicted, including two genes encoding exonuclease family protein, two genes encoding hypothetical protein, and two genes encoding transposon protein. The nucleotide variations and the expression patterns of the candidate genes were identified and analyzed between MSJ13 and MSJ18 through sequence comparison and RT-PCR approach, and results indicated that ORF1 and ORF2 encoding exonuclease family protein might be the causal candidate genes for panicle blast resistance in the qPBR10-1 locus. Conclusions A total of 7 QTLs conferring panicle blast resistance was identified from one F2 population derived from the crossing between two advanced backcross inbred sister lines MSJ13 and MSJ18, which harbored the broad-spectrum resistance gene Pigm. A major QTL qPBR10-1 was fine mapped in a 60.6-kb region with six candidate genes predicted, and ORF1 and ORF2 encoding exonuclease family protein might be the causal candidate genes for panicle blast resistance in the qPBR10-1 locus through sequence comparison and RT-PCR approach.

scholarly journals De novo transcriptome analysis of Lantana camara L. revealed candidate genes involved in phenylpropanoid biosynthesis pathway

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Muzammil Shah ◽  
Hesham F. Alharby ◽  
Khalid Rehman Hakeem ◽  
Niaz Ali ◽  
Inayat Ur Rahman ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Transcriptome Analysis ◽  
De Novo ◽  
Lantana Camara ◽  
Biosynthesis Pathway ◽  
De Novo Transcriptome ◽  
Phenylpropanoid Biosynthesis

scholarly journals Identification, pyramid and candidate genes of QTLs for associated traits based on a dense erect panicle rice CSSL-Z749 and five SSSLs, three DSSLs and one TSSL

Rice ◽  
2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Dachuan Wang ◽  
Kai Zhou ◽  
Siqian Xiang ◽  
Qiuli Zhang ◽  
Ruxiang Li ◽  
...  
Keyword(s):  
Candidate Gene ◽  
Candidate Genes ◽  
Complex Traits ◽  
Seed Set ◽  
Average Length ◽  
Substitution Lines ◽  
Chromosome Segment Substitution Lines ◽  
Minor Qtls ◽  
Segment Substitution ◽  
Major Qtl

Abstract Background Seed-set density is an important agronomic trait in rice. However, its genetic mechanism is complex. Chromosome segment substitution lines (CSSLs) are ideal materials for studying complex traits. Results A rice CSSL, Z749, with a dense and erect panicle phenotype, was identified among progeny of the recipient parent Nipponbare and the donor parent Xihui 18. Z749 carried seven substitution segments (average length 2.12 Mb). Compared with Nipponbare, Z749 showed significant increases in the numbers of primary (NPB) and secondary branches (NSB), number of spikelets (SPP) and grains per panicle (GPP), seed-set density (SSD), and decrease in panicle length (PL). A secondary F2 population derived from a cross between Nipponbare and Z749 was used to map quantitative trait loci (QTLs) for associated traits. Fifteen QTLs distributed on chromosomes 5, 7, 8, and 10 were detected. The QTL qPL7 might be an allele of OsFAD8 and the remaining 14 QTLs (e.g., qSSD5 and qSSD10 etc.) might be novel. Fourteen QTLs were verified using five single-segment substitution lines (SSSLs). The seed-set density of Z749 was controlled predominantly by one major QTL (qSSD10) and two minor QTLs (qSSD5 and qSSD8). The QTLs qSSD10, qSSD5, and qSSD8 were fine-mapped to intervals of 1.05, 1.46, and 1.53 Mb on chromosomes 10, 5, and 8, respectively. Analysis of QTL additive effects indicated that qSSD5, qSSD8, and qSSD10 from Xihui18 increased seed-set density of Z749 by 14.10, 11.38, and 5.11 spikelets per 10 cm panicle, respectively. Analysis of QTL epistatic effects revealed that pyramiding of qSSD5 and qSSD8, qSSD5 and qSSD10, qSSD8 and qSSD10, and qSSD5, qSSD8 and qSSD10 produced novel genotypes with increased seed-set density. Conclusions Inheritance of seed-set density in Z749 was controlled predominantly by one major QTL (qSSD10) and two minor QTLs (qSSD5 and qSSD8). Then, they were fine-mapped to intervals of 1.05, 1.46, and 1.53 Mb on chromosomes 10, 5, 8, respectively. Two MAPK genes (OsMPK9 and OsMPK17) and one gene (candidate gene 6) involved in auxin metabolism might be candidate genes for qSSD5, and OsSAUR32 might be the candidate gene for qSSD8. Pyramiding of qSSD5, qSSD8, and qSSD10 enhanced seed-set density.

scholarly journals Identification of Main-Effect and Environmental Interaction QTL and Their Candidate Genes for Drought Tolerance in a Wheat RIL Population Between Two Elite Spring Cultivars

2021 ◽  
Vol 12 ◽  
Author(s):  
S. M. Hisam Al Rabbi ◽  
Ajay Kumar ◽  
Sepehr Mohajeri Naraghi ◽  
Suraj Sapkota ◽  
Mohammed S. Alamri ◽  
...  
Keyword(s):  
Drought Tolerance ◽  
Candidate Genes ◽  
Phenotypic Variation ◽  
Kernel Weight ◽  
Snp Markers ◽  
Expression Variability ◽  
Volume Weight ◽  
Drought Tolerant ◽  
Ril Population ◽  
Major Qtl

Understanding the genetics of drought tolerance can expedite the development of drought-tolerant cultivars in wheat. In this study, we dissected the genetics of drought tolerance in spring wheat using a recombinant inbred line (RIL) population derived from a cross between a drought-tolerant cultivar, ‘Reeder’ (PI613586), and a high-yielding but drought-susceptible cultivar, ‘Albany.’ The RIL population was evaluated for grain yield (YLD), grain volume weight (GVW), thousand kernel weight (TKW), plant height (PH), and days to heading (DH) at nine different environments. The Infinium 90 k-based high-density genetic map was generated using 10,657 polymorphic SNP markers representing 2,057 unique loci. Quantitative trait loci (QTL) analysis detected a total of 11 consistent QTL for drought tolerance-related traits. Of these, six QTL were exclusively identified in drought-prone environments, and five were constitutive QTL (identified under both drought and normal conditions). One major QTL on chromosome 7B was identified exclusively under drought environments and explained 13.6% of the phenotypic variation (PV) for YLD. Two other major QTL were detected, one each on chromosomes 7B and 2B under drought-prone environments, and explained 14.86 and 13.94% of phenotypic variation for GVW and YLD, respectively. One novel QTL for drought tolerance was identified on chromosome 2D. In silico expression analysis of candidate genes underlaying the exclusive QTLs associated with drought stress identified the enrichment of ribosomal and chloroplast photosynthesis-associated proteins showing the most expression variability, thus possibly contributing to stress response by modulating the glycosyltransferase (TraesCS6A01G116400) and hexosyltransferase (TraesCS7B01G013300) unique genes present in QTL 21 and 24, respectively. While both parents contributed favorable alleles to these QTL, unexpectedly, the high-yielding and less drought-tolerant parent contributed desirable alleles for drought tolerance at four out of six loci. Regardless of the origin, all QTL with significant drought tolerance could assist significantly in the development of drought-tolerant wheat cultivars, using genomics-assisted breeding approaches.

Sequencing of an Anthracnose-Resistant Sorghum Genotype and Mapping of a Major QTL Reveal Strong Candidate Genes for Anthracnose Resistance

Crop Science ◽  
2015 ◽  
Vol 55 (2) ◽  
pp. 790-799 ◽  
Author(s):  
A. Millie Burrell ◽  
Arun Sharma ◽  
Nikhil Y. Patil ◽  
S. Delroy Collins ◽  
William F. Anderson ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Anthracnose Resistance ◽  
Strong Candidate ◽  
Major Qtl

SEED COLOUR IN BRASSICA NAPUS: QTL MAPPING, CANDIDATE GENES AND ASSOCIATIONS WITH QUALITY TRAITS

2006 ◽  
pp. 203-210 ◽  
Author(s):  
A.G. Badani ◽  
B. Wittkop ◽  
W. Lühs ◽  
R. Baetzel ◽  
R. Horn ◽  
...  
Keyword(s):  
Brassica Napus ◽  
Qtl Mapping ◽  
Candidate Genes ◽  
Quality Traits ◽  
Seed Colour

Sex-specific genetic dissection of diabetes in a rodent model identifies Ica1 and Ndufa4 as major candidate genes

2010 ◽  
Vol 42 (3) ◽  
pp. 445-455 ◽  
Author(s):  
Ronit Barkalifa ◽  
Yoram Yagil ◽  
Chana Yagil
Keyword(s):  
Candidate Genes ◽  
Differentially Expressed ◽  
Diabetic Rat ◽  
Genetic Dissection ◽  
Promoter Regions ◽  
F2 Population ◽  
Trait Locus ◽  
Functional Relevance ◽  
Consomic Strain ◽  
Major Qtl

The aim of the study was to initiate a sex-specific investigation of the molecular basis of diabetes, using a genomic approach in the Cohen Diabetic rat model of diet-induced Type 2 diabetes. We used an F2 population resulting from a cross between Cohen Diabetic susceptible (CDs) and resistant (CDr) and consisting of 132 males and 159 females to detect relevant QTLs by linkage and cosegregation analyses. To confirm the functional relevance of the QTL, we applied the “chromosome substitution” strategy. We identified candidate genes within the quantitative trait locus (QTL) and studied their differential expression. We sequenced the differentially expressed candidate genes to account for differences in their expression. We confirmed in this new cross in males a previously detected major QTL on rat chromosome 4 (RNO4); we identified in females this major QTL as well. We found three additional diabetes-related QTLs on RNO11, 13, and 20 in females only. We pursued the investigation of the QTL on RNO4 and generated a CDs.4CDr consomic strain, which provided us with functional confirmation for the contribution of the QTL to the diabetic phenotype in both sexes. We successfully narrowed the QTL span to 2.6 cM and identified within it six candidate genes, but only two of which, Ica1 (islet cell autoantigen 1) and Ndufa4 (NADH dehydrogenase ubiquinone) were differentially expressed between CDs and CDr. We sequenced the exons and promoter regions of Ica1 and Ndufa4 but did not identify sequence variations between the strains. The detection of the QTL on RNO4 in both sexes suggests involvement of Ica1, Ndufa4, the Golgi apparatus, the mitochondria and genetic susceptibility to dietary-environmental factors in the pathophysiology of diabetes in our model. The additional sex-specific QTLs are likely to account for differences in the diabetic phenotype between the sexes.

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