The Genetic Basis of Anthocyanin Acylation in North American Grapes (Vitis spp.)

Hydroxycinnamylated anthocyanins (or simply ‘acylated anthocyanins’) increase color stability in grape products, such as wine. Several genes that are relevant for anthocyanin acylation in grapes have been previously described; however, control of the degree of acylation in grapes is complicated by the lack of genetic markers quantitatively associated with this trait. To characterize the genetic basis of anthocyanin acylation in grapevine, we analyzed the acylation ratio in two closely related biparental families, Vitis rupestris B38 × ‘Horizon’ and ‘Horizon’ × Illinois 547-1, for 2 and 3 years, respectively. The acylation ratio followed a bimodal and skewed distribution in both families, with repeatability estimates larger than 0.84. Quantitative trait locus (QTL) mapping with amplicon-based markers (rhAmpSeq) identified a strong QTL from ‘Horizon’ on chromosome 3, near 15.85 Mb in both families and across years, explaining up to 85.2% of the phenotypic variance. Multiple candidate genes were identified in the 14.85–17.95 Mb interval, in particular, three copies of a gene encoding an acetyl-CoA-benzylalcohol acetyltransferase-like protein within the two most strongly associated markers. Additional population-specific QTLs were found in chromosomes 9, 10, 15, and 16; however, no candidate genes were described. The rhAmpSeq markers reported here, which were previously shown to be highly transferable among the Vitis genus, could be immediately implemented in current grapevine breeding efforts to control the degree of anthocyanin acylation and improve the quality of grapes and their products.

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Quantitative Trait Loci Differentiating the Outbreeding Mimulus guttatus From the Inbreeding M. platycalyx

Genetics ◽

10.1093/genetics/146.3.1115 ◽

1997 ◽

Vol 146 (3) ◽

pp. 1115-1121 ◽

Cited By ~ 3

Author(s):

Jing-Zhong Lin ◽

Kermit Ritland

Keyword(s):

Mating System ◽

Quantitative Trait ◽

Genetic Architecture ◽

Genetic Basis ◽

Random Amplified Polymorphic Dna ◽

Phenotypic Variance ◽

Mimulus Guttatus ◽

Theoretical Predictions ◽

Trait Locus ◽

Plant Mating System

Theoretical predictions about the evolution of selfing depend on the genetic architecture of loci controlling selfing (monogenic vs. polygenic determination, large vs. small effect of alleles, dominance vs. recessiveness), and studies of such architecture are lacking. We inferred the genetic basis of mating system differences between the outbreeding Mimulus guttatus and the inbreeding M. platycalyx by quantitative trait locus (QTL) mapping using random amplified polymorphic DNA and isozyme markers. One to three QTL were detected for each of five mating system characters, and each QTL explained 7.6–28.6% of the phenotypic variance. Taken together, QTL accounted for up to 38% of the variation in mating system characters, and a large proportion of variation was unaccounted for. Inferred QTL often affected more than one trait, contributing to the genetic correlation between those traits. These results are consistent with the hypothesis that quantitative variation in plant mating system characters is primarily controlled by loci with small effect.

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Polygenicity and epistasis underlie fitness-proximal traits in the Caenorhabditis elegans multiparental experimental evolution (CeMEE) panel

10.1101/120865 ◽

2017 ◽

Cited By ~ 2

Author(s):

Luke M. Noble ◽

Ivo Chelo ◽

Thiago Guzella ◽

Bruno Afonso ◽

David D. Riccardi ◽

...

Keyword(s):

Caenorhabditis Elegans ◽

Experimental Evolution ◽

Complex Traits ◽

Genetic Basis ◽

Natural Populations ◽

Phenotypic Variance ◽

Nucleotide Polymorphisms ◽

C Elegans ◽

Mapping Panel ◽

Trait Locus

ABSTRACTUnderstanding the genetic basis of complex traits remains a major challenge in biology. Polygenicity, phenotypic plasticity and epistasis contribute to phenotypic variance in ways that are rarely clear. This uncertainty is problematic for estimating heritability, for predicting individual phenotypes from genomic data, and for parameterizing models of phenotypic evolution. Here we report a recombinant inbred line (RIL) quantitative trait locus (QTL) mapping panel for the hermaphroditic nematode Caenorhabditis elegans, the C. elegans multiparental experimental evolution (CeMEE) panel. The CeMEE panel, comprising 507 RILs, was created by hybridization of 16 wild isolates, experimental evolution at moderate population sizes and predominant outcrossing for 140-190 generations, and inbreeding by selfing for 13-16 generations. The panel contains 22% of single nucleotide polymorphisms known to segregate in natural populations, and complements existing mapping resources for C. elegans by providing high nucleotide diversity across >95% of the genome. We apply it to study the genetic basis of two fitness components, fertility and hermaphrodite body size at time of reproduction, with high broad sense heritability in the CeMEE. While simulations show we should detect common alleles with additive effects as small as 5%, at gene-level resolution, the genetic architectures of these traits does not feature such alleles. We instead find that a significant fraction of trait variance, particularly for fertility, can be explained by sign epistasis with weak main effects. In congruence, phenotype prediction, while generally poor (r2 < 10%), requires modeling epistasis for optimal accuracy, with most variance attributed to the highly recombinant, rapidly evolving chromosome arms.

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Identification of genomic regions and candidate genes of functional importance for gastrointestinal parasite resistance traits in Djallonké sheep of Burkina Faso

Archives Animal Breeding ◽

10.5194/aab-62-313-2019 ◽

2019 ◽

Vol 62 (1) ◽

pp. 313-323

Author(s):

Isabel Álvarez ◽

Iván Fernández ◽

Albert Soudré ◽

Amadou Traoré ◽

Lucía Pérez-Pardal ◽

...

Keyword(s):

Burkina Faso ◽

Candidate Genes ◽

Genetic Basis ◽

Ovis Aries ◽

Enrichment Score ◽

Phenotypic Variance ◽

Potential Candidate ◽

Parasite Resistance ◽

Functional Importance ◽

Resistance Traits

Abstract. A total of 184 Djallonké lambs from Burkina Faso with phenotypes for packed-cell volume (PCV), log-transformed fecal egg count (lnFEC), and FAffa MAlan CHArt (FAMACHA©) eye scores were typed with the OvineSNP50 BeadChip of Illumina to contribute to the knowledge of the genetic basis of gastrointestinal (GIN) parasite resistance in sheep. Association analysis identified a total of 22 single-nucleotide polymorphisms (SNPs) related with PCV (6 SNPs), lnFEC (7), and FAMACHA scores (9) distributed among 14 Ovis aries chromosomes (OAR). The identified SNPs accounted for 18.76 % of the phenotypic variance for PCV, 21.24 % for lnFEC, and 34.38 % for FAMACHA scores. Analyses pointed out the importance of OAR2 for PCV, OAR3 for FAMACHA scores, and OAR6 for lnFEC. The 125 kb regions surrounding the identified SNPs overlapped with seven previously reported quantitative trait loci (QTLs) for the traits analyzed in the current work. The only chromosome harboring markers associated with the three traits studied was OAR2. In agreement with the literature, two different chromosomal areas on OAR2 can play a major role in the traits studied. Gene-annotation enrichment analysis allowed us to identify a total of 34 potential candidate genes for PCV (6 genes), lnFEC (4), and FAMACHA scores (24). Annotation analysis allowed us to identify one functional term cluster with a significant enrichment score (1.302). The cluster included five genes (TRIB3, CDK4, CSNK2A1, MARK1, and SPATA5) involved in immunity-related and cell-proliferation processes. Furthermore, this research suggests that the MBL2 gene can underlie a previously reported QTL for immunoglobulin A levels on OAR22 and confirms the importance of genes involved in growth and size (such as the ADAMTS17 gene on OAR18) for GIN resistance traits. Since association studies for the ascertainment of the genetic basis of GIN resistance may be affected by genotype–environment interactions, obtaining information from local sheep populations managed in harsh environments contributes to the identification of novel genomic areas of functional importance for GIN resistance for that trait.

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Study on fine mapping of QTL for juice yield traits of sweet sorghum (Sorghum dochna)

Czech Journal of Genetics and Plant Breeding ◽

10.17221/48/2021-cjgpb ◽

2022 ◽

Author(s):

Bo Zhao ◽

Buxian Xia ◽

Jianming Gao ◽

Feng Luo ◽

Qiuling Chen ◽

...

Keyword(s):

Sweet Sorghum ◽

Single Gene ◽

Phenotypic Variance ◽

Gene Encoding ◽

Yield And Quality ◽

Economic Production ◽

Juice Yield ◽

Yield Trait ◽

Key Factor ◽

Trait Locus

The stem juice yield is a key factor that influences both the biological and economic production of sweet sorghum [Sorghum dochna (Forssk.) Snowden]. To elucidate upon the genetic basis of the stem juice yield, an F5 population developed from a cross between the low juice yielding Xinliang52 (XL52) and high juice yielding W455 lines, were used in a quantitative trait locus (QTL) analysis. A main effect of the QTL controlling stem juice yield was separated with an SSR marker called Xtxp97, which explained 46.7% of the phenotypic variance. In addition, F5 and F6 populations were constructed with XL52 and W452 as the parents to further verify the QTLs, and a significant correlation was found between the juice yield trait and the Xtxp97 marker. Based on the progeny tests of 29 recombinants, QJy-sbi06 was located in a region of about 21.2 kb on chromosome 6, where a candidate gene encoding an NAC transcription factor (sobic.006G147400) was identified. Combining the different population association analysis and sequencing technology showed that XL52 inserted a 1.8 kb transposon in the NAC to directly interrupt and inactivate the juice yield gene. This study also demonstrated that the colour of the leaf midribs was controlled by a single gene and was significantly positive correlated with juiciness (r = 0.784, P < 0.01). These results could lay the foundation for map-based cloning of QJy-sbi06 and provide genes or QTLs for breeding sorghum lines with a high juice yield and quality.

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O-linked N-acetylglucosamine transferase is involved in fine regulation of flowering time in winter wheat

Nature Communications ◽

10.1038/s41467-021-22564-8 ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Min Fan ◽

Fang Miao ◽

Haiyan Jia ◽

Genqiao Li ◽

Carol Powers ◽

...

Keyword(s):

Winter Wheat ◽

Flowering Time ◽

Heading Date ◽

Wheat Cultivars ◽

Gene Encoding ◽

Constitutive Overexpression ◽

Winter Wheat Cultivars ◽

Fine Regulation ◽

Trait Locus ◽

Glcnac Transferase

AbstractVernalization genes underlying dramatic differences in flowering time between spring wheat and winter wheat have been studied extensively, but little is known about genes that regulate subtler differences in flowering time among winter wheat cultivars, which account for approximately 75% of wheat grown worldwide. Here, we identify a gene encoding anO-linkedN-acetylglucosamine (O-GlcNAc) transferase (OGT) that differentiates heading date between winter wheat cultivars Duster and Billings. We clone thisTaOGT1gene from a quantitative trait locus (QTL) for heading date in a mapping population derived from these two bread wheat cultivars and analyzed in various environments. Transgenic complementation analysis shows that constitutive overexpression ofTaOGT1bfrom Billings accelerates the heading of transgenic Duster plants.TaOGT1 is able to transfer anO-GlcNAc group to wheat proteinTaGRP2. Our findings establish important roles forTaOGT1in winter wheat in adaptation to global warming in the future climate scenarios.

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Inferring Linkage Disequilibrium Between a Polymorphic Marker Locus and a Trait Locus in Natural Populations

Genetics ◽

10.1093/genetics/156.1.457 ◽

2000 ◽

Vol 156 (1) ◽

pp. 457-467 ◽

Cited By ~ 1

Author(s):

Z W Luo ◽

S H Tao ◽

Z-B Zeng

Keyword(s):

Linkage Disequilibrium ◽

Allele Frequency ◽

Random Mating ◽

Natural Populations ◽

Polymorphic Marker ◽

Marker Locus ◽

Model Parameters ◽

Phenotypic Variance ◽

Wide Range ◽

Trait Locus

Abstract Three approaches are proposed in this study for detecting or estimating linkage disequilibrium between a polymorphic marker locus and a locus affecting quantitative genetic variation using the sample from random mating populations. It is shown that the disequilibrium over a wide range of circumstances may be detected with a power of 80% by using phenotypic records and marker genotypes of a few hundred individuals. Comparison of ANOVA and regression methods in this article to the transmission disequilibrium test (TDT) shows that, given the genetic variance explained by the trait locus, the power of TDT depends on the trait allele frequency, whereas the power of ANOVA and regression analyses is relatively independent from the allelic frequency. The TDT method is more powerful when the trait allele frequency is low, but much less powerful when it is high. The likelihood analysis provides reliable estimation of the model parameters when the QTL variance is at least 10% of the phenotypic variance and the sample size of a few hundred is used. Potential use of these estimates in mapping the trait locus is also discussed.

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Linkage mapping identifies a non-synonymous mutation in FLOWERING LOCUS T (FT-B1) increasing spikelet number per spike

Scientific Reports ◽

10.1038/s41598-020-80473-0 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Jonathan Brassac ◽

Quddoos H. Muqaddasi ◽

Jörg Plieske ◽

Martin W. Ganal ◽

Marion S. Röder

Keyword(s):

Flowering Time ◽

Aspartic Acid ◽

Synonymous Substitution ◽

Minor Effect ◽

Phenotypic Variance ◽

Spikelet Number ◽

Wheat Varieties ◽

Trait Locus ◽

A Minor ◽

Spikelet Number Per Spike

AbstractTotal spikelet number per spike (TSN) is a major component of spike architecture in wheat (Triticumaestivum L.). A major and consistent quantitative trait locus (QTL) was discovered for TSN in a doubled haploid spring wheat population grown in the field over 4 years. The QTL on chromosome 7B explained up to 20.5% of phenotypic variance. In its physical interval (7B: 6.37–21.67 Mb), the gene FLOWERINGLOCUST (FT-B1) emerged as candidate for the observed effect. In one of the parental lines, FT-B1 carried a non-synonymous substitution on position 19 of the coding sequence. This mutation modifying an aspartic acid (D) into a histidine (H) occurred in a highly conserved position. The mutation was observed with a frequency of ca. 68% in a set of 135 hexaploid wheat varieties and landraces, while it was not found in other plant species. FT-B1 only showed a minor effect on heading and flowering time (FT) which were dominated by a major QTL on chromosome 5A caused by segregation of the vernalization gene VRN-A1. Individuals carrying the FT-B1 allele with amino acid histidine had, on average, a higher number of spikelets (15.1) than individuals with the aspartic acid allele (14.3) independent of their VRN-A1 allele. We show that the effect of TSN is not mainly related to flowering time; however, the duration of pre-anthesis phases may play a major role.

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Meta-QTL analysis and identification of candidate genes for quality, abiotic and biotic stress in durum wheat

Scientific Reports ◽

10.1038/s41598-021-91446-2 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Jose Miguel Soriano ◽

Pasqualina Colasuonno ◽

Ilaria Marcotuli ◽

Agata Gadaleta

Keyword(s):

Molecular Markers ◽

Abiotic Stress ◽

Durum Wheat ◽

Candidate Genes ◽

Biotic Stress ◽

Qtl Analysis ◽

Complex Traits ◽

Genetic Basis ◽

Agronomic Traits ◽

Plant Performance

AbstractThe genetic improvement of durum wheat and enhancement of plant performance often depend on the identification of stable quantitative trait loci (QTL) and closely linked molecular markers. This is essential for better understanding the genetic basis of important agronomic traits and identifying an effective method for improving selection efficiency in breeding programmes. Meta-QTL analysis is a useful approach for dissecting the genetic basis of complex traits, providing broader allelic coverage and higher mapping resolution for the identification of putative molecular markers to be used in marker-assisted selection. In the present study, extensive QTL meta-analysis was conducted on 45 traits of durum wheat, including quality and biotic and abiotic stress-related traits. A total of 368 QTL distributed on all 14 chromosomes of genomes A and B were projected: 171 corresponded to quality-related traits, 127 to abiotic stress and 71 to biotic stress, of which 318 were grouped in 85 meta-QTL (MQTL), 24 remained as single QTL and 26 were not assigned to any MQTL. The number of MQTL per chromosome ranged from 4 in chromosomes 1A and 6A to 9 in chromosome 7B; chromosomes 3A and 7A showed the highest number of individual QTL (4), and chromosome 7B the highest number of undefined QTL (4). The recently published genome sequence of durum wheat was used to search for candidate genes within the MQTL peaks. This work will facilitate cloning and pyramiding of QTL to develop new cultivars with specific quantitative traits and speed up breeding programs.

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Quantitative Trait Loci for Susceptibility to Tapeworm Infection in the Red Flour Beetle

Genetics ◽

10.1093/genetics/165.3.1307 ◽

2003 ◽

Vol 165 (3) ◽

pp. 1307-1315

Author(s):

Daibin Zhong ◽

Aditi Pai ◽

Guiyun Yan

Keyword(s):

Quantitative Trait Loci ◽

Quantitative Trait ◽

Genetic Basis ◽

Life Cycles ◽

Red Flour Beetle ◽

Phenotypic Variance ◽

Flour Beetle ◽

Trait Loci ◽

Host Ecology ◽

Tapeworm Infection

Abstract Parasites have profound effects on host ecology and evolution, and the effects of parasites on host ecology are often influenced by the magnitude of host susceptibility to parasites. Many parasites have complex life cycles that require intermediate hosts for their transmission, but little is known about the genetic basis of the intermediate host's susceptibility to these parasites. This study examined the genetic basis of susceptibility to a tapeworm (Hymenolepis diminuta) in the red flour beetle (Tribolium castaneum) that serves as an intermediate host in its transmission. Quantitative trait loci (QTL) mapping experiments were conducted with two independent segregating populations using amplified fragment length polymorphism (AFLP) markers and randomly amplified polymorphic DNA (RAPD) markers. A total of five QTL that significantly affected beetle susceptibility were identified in the two reciprocal crosses. Two common QTL on linkage groups 3 and 6 were identified in both crosses with similar effects on the phenotype, and three QTL were unique to each cross. In one cross, the three main QTL accounted for 29% of the total phenotypic variance and digenic epistasis explained 39% of the variance. In the second cross, the four main QTL explained 62% of the variance and digenic epistasis accounted for only 5% of the variance. The actions of these QTL were either overdominance or underdominance. Our results suggest that the polygenic nature of beetle susceptibility to the parasites and epistasis are important genetic mechanisms for the maintenance of variation within or among beetle strains in susceptibility to tapeworm infection.

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