Success and failure in replication of genotype–phenotype associations: How does replication help in understanding the genetic basis of phenotypic variation in outbred populations?

Increasing the understanding genetic basis of the variability in root system architecture (RSA) is essential to improve resource-use efficiency in agriculture systems and to develop climate-resilient crop cultivars. Roots being underground, their direct observation and detailed characterization are challenging. Here, were characterized twelve RSA-related traits in a panel of 137 early maturing soybean lines (Canadian soybean core collection) using rhizoboxes and two-dimensional imaging. Significant phenotypic variation (P < 0.001) was observed among these lines for different RSA-related traits. This panel was genotyped with 2.18 million genome-wide single-nucleotide polymorphisms (SNPs) using a combination of genotyping-by-sequencing and whole-genome sequencing. A total of 10 quantitative trait locus (QTL) regions were detected for root total length and primary root diameter through a comprehensive genome-wide association study. These QTL regions explained from 15 to 25% of the phenotypic variation and contained two putative candidate genes with homology to genes previously reported to play a role in RSA in other species. These genes can serve to accelerate future efforts aimed to dissect genetic architecture of RSA and breed more resilient varieties.

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Genetic analysis of three maize husk traits by QTL mapping in a maize-teosinte population

BMC Genomics ◽

10.1186/s12864-021-07723-x ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Xiaolei Zhang ◽

Ming Lu ◽

Aiai Xia ◽

Tao Xu ◽

Zhenhai Cui ◽

...

Keyword(s):

Phenotypic Variation ◽

Genetic Basis ◽

Molecular Breeding ◽

Best Linear Unbiased Predictor ◽

Maize Line ◽

Maize Varieties ◽

Outer Covering ◽

High Heritability ◽

Best Linear Unbiased ◽

Variation Explained

Abstract Background The maize husk consists of numerous leafy layers and plays vital roles in protecting the ear from pathogen infection and dehydration. Teosinte, the wild ancestor of maize, has about three layers of small husk outer covering the ear. Although several quantitative trait loci (QTL) underlying husk morphology variation have been reported, the genetic basis of husk traits between teosinte and maize remains unclear. Results A linkage population including 191 BC2F8 inbred lines generated from the maize line Mo17 and the teosinte line X26–4 was used to identify QTL associated with three husk traits: i.e., husk length (HL), husk width (HW) and the number of husk layers (HN). The best linear unbiased predictor (BLUP) depicted wide phenotypic variation and high heritability of all three traits. The HL exhibited greater correlation with HW than HN. A total of 4 QTLs were identified including 1, 1, 2, which are associated with HL, HW and HN, respectively. The proportion of phenotypic variation explained by these QTLs was 9.6, 8.9 and 8.1% for HL, HN and HW, respectively. Conclusions The QTLs identified in this study will pave a path to explore candidate genes regulating husk growth and development, and benefit the molecular breeding program based on molecular marker-assisted selection to cultivate maize varieties with an ideal husk morphology.

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Genetic Architecture: Dissecting the Genetic Basis of Phenotypic Variation

Current Biology ◽

10.1016/s0960-9822(02)00911-9 ◽

2002 ◽

Vol 12 (12) ◽

pp. R415-R416 ◽

Cited By ~ 5

Author(s):

Julian K Christians ◽

Peter D Keightley

Keyword(s):

Phenotypic Variation ◽

Genetic Architecture ◽

Genetic Basis

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Phenotypic variation in Heliconius erato crosses shows that iridescent structural colour is sex-linked and controlled by multiple genes

Interface Focus ◽

10.1098/rsfs.2018.0047 ◽

2018 ◽

Vol 9 (1) ◽

pp. 20180047 ◽

Cited By ~ 9

Author(s):

Melanie N. Brien ◽

Juan Enciso-Romero ◽

Andrew J. Parnell ◽

Patricio A. Salazar ◽

Carlos Morochz ◽

...

Keyword(s):

Phenotypic Variation ◽

Genetic Basis ◽

Sex Chromosome ◽

Scattering Data ◽

Colour Pattern ◽

Structural Colour ◽

X Ray Scattering ◽

Multiple Genes ◽

Colour Patterns ◽

Blue Reflectance

Bright, highly reflective iridescent colours can be seen across nature and are produced by the scattering of light from nanostructures. Heliconius butterflies have been widely studied for their diversity and mimicry of wing colour patterns. Despite iridescence evolving multiple times in this genus, little is known about the genetic basis of the colour and the development of the structures which produce it. Heliconius erato can be found across Central and South America, but only races found in western Ecuador and Colombia have developed blue iridescent colour. Here, we use crosses between iridescent and non-iridescent races of H. erato to study phenotypic variation in the resulting F 2 generation. Using measurements of blue colour from photographs, we find that iridescent structural colour is a quantitative trait controlled by multiple genes, with strong evidence for loci on the Z sex chromosome. Iridescence is not linked to the Mendelian colour pattern locus that also segregates in these crosses (controlled by the gene cortex ). Small-angle X-ray scattering data show that spacing between longitudinal ridges on the scales, which affects the intensity of the blue reflectance, also varies quantitatively in F 2 crosses.

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Genome-Wide Association Studies of Leaf Angle in Maize

10.21203/rs.3.rs-329481/v1 ◽

2021 ◽

Author(s):

Bo Peng ◽

Xiaolei Zhao ◽

Yi Wang ◽

Chunhui Li ◽

Yongxiang Li ◽

...

Keyword(s):

Candidate Genes ◽

Phenotypic Variation ◽

Genetic Basis ◽

Genome Wide Association ◽

Leaf Angle ◽

Genome Wide Association Studies ◽

Major Qtls ◽

Genome Wide ◽

Population Structure Analysis ◽

A Genome

Abstract Compact plant-type with small leaf angle has increased canopy light interception, which is conducive to the photosynthesis of the population and higher population yield at high density planting in maize. In this study, a panel of 285 diverse maize inbred lines genotyped with 56,000 SNPs was used to investigate the genetic basis of leaf angle across three consecutive years using a genome-wide association study (GWAS). The leaf angle showed broad phenotypic variation and high heritability across different years. Population structure analysis subdivided the panel into four subgroups that correspond to the four major empirical germplasm origins in China, i.e., Tangsipingtou, Reid, Lancaster and P. When tested with the optimal GWAS model, we found that the Q+K model was the best in reducing false positive. In total, 96 SNPs accounting for 5.54%-10.44% of phenotypic variation were significantly (P<0.0001) associated with leaf angle across three years. According to the linkage disequilibrium decay distance, 96 SNPs were binned in 43 QTLs for leaf angle. Seven major QTLs with R2>8% stably detected in at least two years and BLUP values were clustered in four genomic regions (bins 2.01, 2.07, 5.06, and 10.04). Seven important candidate genes, Zm00001d001961, Zm00001d006348, Zm00001d006463, Zm00001d017618, Zm00001d024919, Zm00001d025018, and Zm00001d025033 were predicted for the seven stable major QTLs, respectively. The markers identified in this study can be used for molecular breeding for leaf angle, and the candidate genes would contribute to further understanding of the genetic basis of leaf angle.

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Identification of candidate genes for gelatinization temperature, gel consistency and pericarp color by GWAS in rice based on SLAF-sequencing

10.1101/258244 ◽

2018 ◽

Author(s):

Xinghai Yang ◽

Xiuzhong Xia ◽

Yu Zeng ◽

Baoxuan Nong ◽

Zongqiong Zhang ◽

...

Keyword(s):

Population Structure ◽

Phenotypic Variation ◽

Genetic Basis ◽

Chromosome 3 ◽

Chromosome 6 ◽

Gelatinization Temperature ◽

Rice Landraces ◽

Population Structure Analysis ◽

Pericarp Color ◽

Gel Consistency

AbstractRice is an important cereal in the world, uncovering the genetic basis of agronomic traits in rice landraces genes associated with agronomically important traits is indispensable for both understanding the genetic basis of phenotypic variation and efficient crop improvement. Gelatinization temperature, gel consistency and pericarp color are important indices of rice cooking and eating quality evaluation and potential nutritional importance, which attract wide attentions in the application of genetic and breeding. To dissect the genetic basis of gelatinization temperature (GT), gel consistency (GC) and pericarp color (PC), a total of 419 rice landraces core germplasm collections consisting of 330 indica lines, 78 japonica lines and 11 uncertain varieties were grown, collected, then GT, GC, PC were measured for two years, and sequenced using Specific Locus Amplified Fragment Sequencing (SLAF) technology. In this study, 261,385,070 clean reads and 56,768 polymorphic SLAF tags were obtained, which a total of 211,818 single nucleotide polymorphisms (SNPs) were discovered. With 208,993 SNPs meeting the criterion of minor allele frequency (MAF) > 0.05 and integrity> 0.5, the phylogenetic tree and population structure analysis were performed for all 419 rice landraces, and the whole panel mainly separated into six subpopulations based on population structure analysis. Genome-wide association study (GWAS) was carried out for the whole panel, indica subpanel and japonica subpanel with subset SNPs respectively. One quantitative trait locus (QTL) on chromosome 6 for GT was detected in the whole panel and indica subpanel, and one QTL associated with GC was located on chromosome 6 in the whole panel and indica subpanel. For the PC trait, 8 QTLs were detected in the whole panel on chromosome 1, 3, 4, 7, 8, 10 and 11, and 7 QTLs in the indica subpanel on chromosome 3, 4, 7, 8, 10 and 11. The loci on chromosome 3, 8, 10 and 11 have not been identified previously, and they may be the candidate genes of pericarp color. For the three traits, no QTL was detected in japonica subpanel probably because of the polymorphism repartition between the subpanel, or small population size of japonica subpanel. This paper provides new gene resources and insights into the molecular mechanisms of important agricultural trait of rice phenotypic variation and genetic improvement of rice quality variety breeding.

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Utility of BoCAL-a and BoAP1-a Genotypes in Identifying Broccoli and Cauliflower Accessions

HortScience ◽

10.21273/hortsci.39.4.773c ◽

2004 ◽

Vol 39 (4) ◽

pp. 773C-773

Author(s):

Joanne A. Labate ◽

Larry D. Robertson ◽

Thomas Bjorkman*

Keyword(s):

Brassica Oleracea ◽

Phenotypic Variation ◽

Genetic Basis ◽

Intermediate Phenotype ◽

Flower Buds ◽

Stable Intermediate ◽

Floral Differentiation ◽

Combined Genotypes ◽

Botanical Varieties

Broccoli and cauliflower are different botanical varieties of Brassica oleracea. Mutant alleles at the loci BoCAL and BoAP1 can cause arrest at curding that is characteristic of cauliflower. These genes control early floral differentiation, necessary for the progression from a cauliflower-like inflorescence to the flower buds of broccoli. To what extent is the cauliflower-to-broccoli variation within the USDA-PGRU collection determined by mutant alleles of these genes? We surveyed the broccoli collection to examine the correlation between genotype and phenotype. Earlier work showed that BoCAL alone was not an effective predictor of cauliflower phenotype in this collection. The redundant function of BoCAL and BoAP1 in determining inflorescence arrest raises the possibilty that the combined genotype can explain the phenotypic variation. We found that not to be the case. Two accessions varied in phenotype and segregated at both loci, but the combined genotypes were not associated with the expected phenotypes. Two additional accesssion varied in phenotype and segregated at one locus, but with no association between genotype and phenotype. One line varying widely in phenotype was fixed for both loci. One line that was a stable intermediate phenotype segregated for BoCAL. A commercial broccoli cultivar had the cauliflower allele at both loci. The genetic basis of the cauliflower phenotype in the USDA B. oleracea collection is due more to alleles of genes affecting the expression of BoAP1 adn BoCAL than to variation in these alleles of the genes themselves.

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Variance Components and Estimates of Broad-sense Heritability of Nut and Kernel Traits in Hazelnut

HortScience ◽

10.21273/hortsci.32.3.494d ◽

1997 ◽

Vol 32 (3) ◽

pp. 494D-494

Author(s):

Qiang Yao ◽

Shawn A. Mehlenbacher

Keyword(s):

Genetic Variation ◽

Phenotypic Variation ◽

Variance Components ◽

Genetic Basis ◽

Corylus Avellana ◽

Broad Sense ◽

Broad Sense Heritability ◽

Narrow Sense ◽

High Heritability ◽

Kernel Traits

Seventy-seven trees representing 41 hazelnut (Corylus avellana L.) genotypes were to evaluate variance components and broad-sense heritability for 10 nut and kernel traits from 1994 to 1996. All effects in the models were assumed to be random. All traits had extremely high heritability. This indicated that nearly all of the phenotypic variation had a genetic basis. Knowledge of variance components may help us efficiently allocate resources. Broad-sense heritability estimates were larger than those in narrow sense, suggesting the presence of nonadditive genetic variation in the population.

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Genomic regions controlling shape variation in the first upper molar of the house mouse

eLife ◽

10.7554/elife.29510 ◽

2017 ◽

Vol 6 ◽

Cited By ~ 1

Author(s):

Luisa F Pallares ◽

Ronan Ledevin ◽

Sophie Pantalacci ◽

Leslie M Turner ◽

Eirikur Steingrimsson ◽

...

Keyword(s):

Phenotypic Variation ◽

Genetic Basis ◽

Genome Wide Association Study ◽

Shape Variation ◽

Tooth Shape ◽

Mus Musculus Musculus ◽

Genome Wide ◽

Genomic Regions ◽

Hybrid Mice ◽

Upper Molar

Numerous loci of large effect have been shown to underlie phenotypic variation between species. However, loci with subtle effects are presumably more frequently involved in microevolutionary processes but have rarely been discovered. We explore the genetic basis of shape variation in the first upper molar of hybrid mice between Mus musculus musculus and M. m. domesticus. We performed the first genome-wide association study for molar shape and used 3D surface morphometrics to quantify subtle variation between individuals. We show that many loci of small effect underlie phenotypic variation, and identify five genomic regions associated with tooth shape; one region contained the gene microphthalmia-associated transcription factor Mitf that has previously been associated with tooth malformations. Using a panel of five mutant laboratory strains, we show the effect of the Mitf gene on tooth shape. This is the first report of a gene causing subtle but consistent variation in tooth shape resembling variation in nature.

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An association between tongue-rolling phenotypes and subjects of study of undergraduates

Journal of Biosocial Science ◽

10.1017/s0021932000012244 ◽

1979 ◽

Vol 11 (2) ◽

pp. 193-199 ◽

Cited By ~ 7

Author(s):

C. Azimi-Garakani ◽

J. A. Beardmore

Keyword(s):

Phenotypic Variation ◽

Genetic Basis ◽

Life Sciences ◽

Personality Characteristics ◽

The Arts ◽

Two Samples ◽

University Undergraduates

SummaryThe distribution of phenotypes in the tongue-rolling polymorphism in two samples of university undergraduates, totalling 1066 individuals, shows no difference between the sexes but large differences between groups drawn from different faculties and particularly between the life sciences and the arts. There are also indications of a difference in distribution between arts students living in halls of residence and those living elsewhere.The genetics of tongue-rolling is not yet critically established but, on the assumption that most of the phenotypic variation observed has a genetic basis, the data suggest that the loci governing this character may also contribute to variation in personality characteristics which influence choice of subject of study.

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