Genomic Dissection of Anthracnose (Colletotrichum sublineolum) Resistance Response in Sorghum Differential Line SC112-14

Sorghum production is expanding to warmer and more humid regions where its production is being limited by multiple fungal pathogens. Anthracnose, caused by Colletotrichum sublineolum, is one of the major diseases in these regions, where it can cause yield losses of both grain and biomass. In this study, 114 recombinant inbred lines (RILs) derived from resistant sorghum line SC112-14 were evaluated at four distinct geographic locations in the United States for response to anthracnose. A genome scan using a high-density linkage map of 3,838 single nucleotide polymorphisms (SNPs) detected two loci at 5.25 and 1.18 Mb on chromosomes 5 and 6, respectively, that explain up to 59% and 44% of the observed phenotypic variation. A bin-mapping approach using a subset of 31 highly informative RILs was employed to determine the disease response to inoculation with ten anthracnose pathotypes in the greenhouse. A genome scan showed that the 5.25 Mb region on chromosome 5 is associated with a resistance response to nine pathotypes. Five SNP markers were developed and used to fine map the locus on chromosome 5 by evaluating 1,500 segregating F2:3 progenies. Based on the genotypic and phenotypic analyses of 11 recombinants, the locus was narrowed down to a 470-kb genomic region. Following a genome-wide association study based on 574 accessions previously phenotyped and genotyped, the resistance locus was delimited to a 34-kb genomic interval with five candidate genes. All five candidate genes encode proteins associated with plant immune systems, suggesting they may act in synergy in the resistance response.

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Novel Organ-Specific Genetic Factors for Quantitative Resistance to Late Blight in Potato

10.1101/567289 ◽

2019 ◽

Author(s):

Deissy Katherine Juyo Rojas ◽

Johana Carolina Soto Sedano ◽

Agim Ballvora ◽

Jens Léon ◽

Teresa Mosquera Vásquez

Keyword(s):

Late Blight ◽

Candidate Genes ◽

Genome Wide Association Study ◽

Quantitative Resistance ◽

Genotyping By Sequencing ◽

Phenotypic Variance ◽

Resistance Response ◽

Genome Wide ◽

A Genome ◽

Organ Specific

AbstractPotato, Solanum tuberosum, is one of the highest consumed food in the world, being the basis of the diet of millions of people. The main limiting and destructive disease of potato is late blight, caused by Phytophtora infestans. Here, we present a multi-environmental analysis of the response to P. infestans using an association panel of 150 accessions of S. tuberosum Group Phureja, evaluated in two localities in Colombia. Disease resistance data were merged with a genotyping matrix of 83,862 SNPs obtained by 2b-restriction site–associated DNA and Genotyping by sequencing approaches into a Genome-wide association study. We are reporting 16 organ-specific QTL conferring resistance to late blight. These QTL explain from 13.7% to 50.9% of the phenotypic variance. Six and ten QTL were detected for resistance response in leaves and stem, respectively. In silico analysis revealed 15 candidate genes for resistance to late blight. Four of them have no functional genome annotation, while eleven candidate genes code for diverse proteins, including one leucine-rich repeat kinase.

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Genome-Wide Association Study for Plant Architecture and Bioenergy Traits in Diverse Sorghum and Sudangrass Germplasm

Agronomy ◽

10.3390/agronomy10101602 ◽

2020 ◽

Vol 10 (10) ◽

pp. 1602

Author(s):

Feng Luo ◽

Zhongyou Pei ◽

Xiongwei Zhao ◽

Huifen Liu ◽

Yiwei Jiang ◽

...

Keyword(s):

Association Study ◽

Candidate Genes ◽

Sweet Sorghum ◽

Plant Architecture ◽

Genome Wide Association Study ◽

Recombinant Inbred Lines ◽

Genome Wide Association ◽

Phenotypic Traits ◽

Genome Wide ◽

A Genome

Sorghum is an important grain, forage, and bioenergy crop. The objective of this study was to identify genetic signals associated with plant architecture and bioenergy traits in sorghum and sudangrass germplasm through a genome-wide association study (GWAS). Plant height (HT), tiller number (TN), internode number (IN), stem diameter (SD), panicle length (PL), panicle weight (PW), reducing sugar (RS) content, Brix, and protein (PRO) content were assessed in 300 germplasm consisting of grain sorghum, sweet sorghum, sudangrass, sweet sorghum-sweet sorghum recombinant inbred lines (RILs) and sudangrass-sudangrass RILs grown in three different environments over two years. Large variations of phenotypic traits were observed in the population panel. The heritability of traits were all higher than 0.5, ranging from 0.52 (PRO) to 0.92 (HT) with an average of 0.76. The population exhibited three population structures (Q) and minor relative kinship (K), assessed by using 7982 single-nucleotide polymorphisms (SNPs). After controlling Q and K, GWAS identified 24 SNPs that were significantly associated with traits, including three SNPs with HT, four with TN, four with PL, three with Brix, and ten with RS. Of them, seven SNPs were novel signals that were not identified previously, including one for HT, one for TN, one for Brix, and four for RS. The putative candidate genes involved in brassinosteroid regulatory pathway, auxin biosynthesis, carbohydrate metabolism, and sugar transport were identified underlying the significant SNPs. Identification of SNP signals and related candidate genes would enrich the current genomic resource for further molecular breeding aimed at improvement of food, feed, and biofuel productions of sorghum.

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Identification of potential genes for resistance to tomato spotted wilt and leaf spots in peanut (Arachis hypogaea L.) through GWAS analysis

10.21203/rs.2.9597/v1 ◽

2019 ◽

Author(s):

Hui Zhang ◽

Ye Chu ◽

Phat Dang ◽

Yueyi Tang ◽

Jing Li ◽

...

Keyword(s):

Candidate Genes ◽

Leaf Spot ◽

Genome Wide Association Study ◽

Snp Array ◽

The United States ◽

Economic Losses ◽

Major Qtls ◽

Tomato Spotted Wilt ◽

A Genome ◽

Genomic Regions

Abstract Background Tomato spotted wilt (TSW), early leaf spot (ELS), and late leaf spot (LLS) are three serious peanut diseases in the United States, causing tens of millions of dollars of annual economic losses. However, the genes underlying resistance to those diseases in peanut have not been well studied. We conducted a genome-wide association study (GWAS) for the three peanut diseases using Affymetrix version 2.0 SNP array with 120 genotypes mainly coming from the U.S. peanut mini core collection. Results A total of 87 quantitative trait loci (QTLs) were identified with phenotypic variation explained (PVE) from 10.2% to 24.1%, in which 41 QTLs are for resistance to TSW, 18 QTLs for ELS, and 28 QTLs for LLS. Among the 87 QTLs, there were six, four, and two major QTLs with PVE higher than 14.9% for resistance to TSW, ELS, and LLS, respectively. Of the 12 major QTLs, 10 were located on the B sub-genome and only 2 were on the A sub-genome, which suggested that the B sub-genome has more significantly resistance genomic regions than the A sub-genome. In addition, two genomic regions on linkage group B09 were found to provide significant resistance to both ELS and LLS. A total of 22 non-redundant candidate genes were identified significantly associated with diseases, which include 18 candidate genes for TSW, 3 candidate genes for both ELS and LLS, and 1 candidate gene for LLS, respectively. Conclusions Most candidate genes in the associated regions are known to be involved in immunity and defense response. The QTLs and candidate genes obtained from this study will be useful to breed peanut for resistances to the diseases.

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The Genetic Architecture of Ovariole Number in Drosophila melanogaster: Genes with Major, Quantitative, and Pleiotropic Effects

G3 Genes|Genome|Genetics ◽

10.1534/g3.117.042390 ◽

2017 ◽

Vol 7 (7) ◽

pp. 2391-2403 ◽

Cited By ~ 11

Author(s):

Amanda S Lobell ◽

Rachel R Kaspari ◽

Yazmin L Serrano Negron ◽

Susan T Harbison

Keyword(s):

Candidate Genes ◽

Genome Wide Association Study ◽

Natural Populations ◽

Direct Role ◽

Genome Wide ◽

A Genome ◽

Fitness Trait ◽

Sleep Parameters ◽

Activity Behavior ◽

Ovariole Number

Abstract Ovariole number has a direct role in the number of eggs produced by an insect, suggesting that it is a key morphological fitness trait. Many studies have documented the variability of ovariole number and its relationship to other fitness and life-history traits in natural populations of Drosophila. However, the genes contributing to this variability are largely unknown. Here, we conducted a genome-wide association study of ovariole number in a natural population of flies. Using mutations and RNAi-mediated knockdown, we confirmed the effects of 24 candidate genes on ovariole number, including a novel gene, anneboleyn (formerly CG32000), that impacts both ovariole morphology and numbers of offspring produced. We also identified pleiotropic genes between ovariole number traits and sleep and activity behavior. While few polymorphisms overlapped between sleep parameters and ovariole number, 39 candidate genes were nevertheless in common. We verified the effects of seven genes on both ovariole number and sleep: bin3, blot, CG42389, kirre, slim, VAChT, and zfh1. Linkage disequilibrium among the polymorphisms in these common genes was low, suggesting that these polymorphisms may evolve independently.

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Genome-Wide Association Analysis of Growth Curve Parameters in Chinese Simmental Beef Cattle

Animals ◽

10.3390/ani11010192 ◽

2021 ◽

Vol 11 (1) ◽

pp. 192

Author(s):

Xinghai Duan ◽

Bingxing An ◽

Lili Du ◽

Tianpeng Chang ◽

Mang Liang ◽

...

Keyword(s):

Beef Cattle ◽

Candidate Genes ◽

Growth Curve ◽

Growth And Development ◽

Genome Wide Association Study ◽

Genome Wide Association ◽

Coefficient Of Determination ◽

Nucleotide Polymorphisms ◽

Genome Wide ◽

A Genome

The objective of the present study was to perform a genome-wide association study (GWAS) for growth curve parameters using nonlinear models that fit original weight–age records. In this study, data from 808 Chinese Simmental beef cattle that were weighed at 0, 6, 12, and 18 months of age were used to fit the growth curve. The Gompertz model showed the highest coefficient of determination (R2 = 0.954). The parameters’ mature body weight (A), time-scale parameter (b), and maturity rate (K) were treated as phenotypes for single-trait GWAS and multi-trait GWAS. In total, 9, 49, and 7 significant SNPs associated with A, b, and K were identified by single-trait GWAS; 22 significant single nucleotide polymorphisms (SNPs) were identified by multi-trait GWAS. Among them, we observed several candidate genes, including PLIN3, KCNS3, TMCO1, PRKAG3, ANGPTL2, IGF-1, SHISA9, and STK3, which were previously reported to associate with growth and development. Further research for these candidate genes may be useful for exploring the full genetic architecture underlying growth and development traits in livestock.

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Genome-Wide Association Study Reveals the Genetic Basis of Cold Tolerance in Rice at the Seedling Stage

Agriculture ◽

10.3390/agriculture11040318 ◽

2021 ◽

Vol 11 (4) ◽

pp. 318

Author(s):

Tae-Ho Ham ◽

Yebin Kwon ◽

Yoonjung Lee ◽

Jisu Choi ◽

Joohyun Lee

Keyword(s):

Association Study ◽

Candidate Genes ◽

Cold Tolerance ◽

Genome Wide Association Study ◽

Seedling Stage ◽

Genome Wide Association ◽

Matrix Analysis ◽

Rice Seedlings ◽

Genome Wide ◽

A Genome

We conducted a genome-wide association study (GWAS) of cold tolerance in a collection of 127 rice accessions, including 57 Korean landraces at the seedling stage. Cold tolerance of rice seedlings was evaluated in a growth chamber under controlled conditions and scored on a 0–9 scale, based on their low-temperature response and subsequent recovery. GWAS, together with principal component analysis (PCA) and kinship matrix analysis, revealed four quantitative trait loci (QTLs) on chromosomes 1, 4, and 5 that explained 16.5% to 18.5% of the variance in cold tolerance. The genomic region underlying the QTL on chromosome four overlapped with a previously reported QTL associated with cold tolerance in rice seedlings. Similarly, one of the QTLs identified on chromosome five overlapped with a previously reported QTL associated with seedling vigor. Subsequent bioinformatic and haplotype analyses revealed three candidate genes affecting cold tolerance within the linkage disequilibrium (LD) block of these QTLs: Os01g0357800, encoding a pentatricopeptide repeat (PPR) domain-containing protein; Os05g0171300, encoding a plastidial ADP-glucose transporter; and Os05g0400200, encoding a retrotransposon protein, Ty1-copia subclass. The detected QTLs and further evaluation of these candidate genes in the future will provide strategies for developing cold-tolerant rice in breeding programs.

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Genetic basis and identification of candidate genes for wooden breast and white striping in commercial broiler chickens

Scientific Reports ◽

10.1038/s41598-021-86176-4 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Juniper A. Lake ◽

Jack C. M. Dekkers ◽

Behnam Abasht

Keyword(s):

Candidate Genes ◽

Broiler Chickens ◽

Genetic Basis ◽

Genome Wide Association Study ◽

Specific Protein ◽

Chromosome 11 ◽

A Genome ◽

White Striping ◽

Commercial Broiler ◽

Wooden Breast

AbstractWooden breast (WB) and white striping (WS) are highly prevalent and economically damaging muscle disorders of modern commercial broiler chickens characterized respectively by palpable firmness and fatty white striations running parallel to the muscle fiber. High feed efficiency and rapid growth, especially of the breast muscle, are believed to contribute to development of such muscle defects; however, their etiology remains poorly understood. To gain insight into the genetic basis of these myopathies, a genome-wide association study was conducted using a commercial crossbred broiler population (n = 1193). Heritability was estimated at 0.5 for WB and WS with high genetic correlation between them (0.88). GWAS revealed 28 quantitative trait loci (QTL) on five chromosomes for WB and 6 QTL on one chromosome for WS, with the majority of QTL for both myopathies located in a ~ 8 Mb region of chromosome 5. This region has highly conserved synteny with a portion of human chromosome 11 containing a cluster of imprinted genes associated with growth and metabolic disorders such as type 2 diabetes and Beckwith-Wiedemann syndrome. Candidate genes include potassium voltage-gated channel subfamily Q member 1 (KCNQ1), involved in insulin secretion and cardiac electrical activity, lymphocyte-specific protein 1 (LSP1), involved in inflammation and immune response.

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Evaluation of candidate genes in a genome-wide association study of childhood asthma in Mexicans

Journal of Allergy and Clinical Immunology ◽

10.1016/j.jaci.2009.09.007 ◽

2010 ◽

Vol 125 (2) ◽

pp. 321-327.e13 ◽

Cited By ~ 60

Author(s):

Hao Wu ◽

Isabelle Romieu ◽

Min Shi ◽

Dana B. Hancock ◽

Huiling Li ◽

...

Keyword(s):

Association Study ◽

Candidate Genes ◽

Childhood Asthma ◽

Genome Wide Association Study ◽

Genome Wide Association ◽

Genome Wide ◽

A Genome

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A genome scan for candidate genes involved in the adaptation of turbot (Scophthalmus maximus)

Marine Genomics ◽

10.1016/j.margen.2015.04.011 ◽

2015 ◽

Vol 23 ◽

pp. 77-86 ◽

Cited By ~ 19

Author(s):

Román Vilas ◽

Sara G. Vandamme ◽

Manuel Vera ◽

Carmen Bouza ◽

Gregory E. Maes ◽

...

Keyword(s):

Candidate Genes ◽

Genome Scan ◽

Scophthalmus Maximus ◽

A Genome ◽

Turbot Scophthalmus Maximus

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Genome-wide association analysis of resistance to Pseudoperonospora cubensis in citron watermelon

Plant Disease ◽

10.1094/pdis-08-21-1611-re ◽

2021 ◽

Author(s):

Dennis Katuuramu ◽

Sandra Branham ◽

Amnon Levi ◽

Patrick Wechter

Keyword(s):

Candidate Genes ◽

Genome Wide Association Study ◽

Citrullus Lanatus ◽

Phenotypic Variability ◽

Germplasm Collection ◽

Snp Markers ◽

Genome Wide Association ◽

Pseudoperonospora Cubensis ◽

Genome Wide ◽

A Genome

Cultivated sweet watermelon (Citrullus lanatus) is an important vegetable crop for millions of people around the world. There are limited sources of resistance to economically important diseases within C. lanatus, whereas Citrullus amarus has a reservoir of traits that can be exploited to improve C. lanatus for resistance to biotic and abiotic stresses. Cucurbit downy mildew (CDM), caused by Pseudoperonospora cubensis, is an emerging threat to watermelon production. We screened 122 C. amarus accessions for resistance to CDM over two tests (environments). The accessions were genotyped by whole-genome resequencing to generate 2,126,759 single nucleotide polymorphic (SNP) markers. A genome-wide association study was deployed to uncover marker-trait associations and identify candidate genes underlying resistance to CDM. Our results indicate the presence of wide phenotypic variability (1.1 - 57.8%) for leaf area infection, representing a 50.7-fold variation for CDM resistance across the C. amarus germplasm collection. Broad-sense heritability estimate was 0.55, implying the presence of moderate genetic effects for resistance to CDM. The peak SNP markers associated with resistance to P. cubensis were located on chromosomes Ca03, Ca05, Ca07, and Ca11. The significant SNP markers accounted for up to 30% of the phenotypic variation and were associated with promising candidate genes encoding disease resistance proteins, leucine-rich repeat receptor-like protein kinase, and WRKY transcription factor. This information will be useful in understanding the genetic architecture of the P. cubensis-Citrullus spp. patho-system as well as development of resources for genomics-assisted breeding for resistance to CDM in watermelon.

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