Genome-wide association analysis of anthracnose resistance in sorghum [Sorghum bicolor (L.) Moench]

In warm-humid ago-ecologies of the world, sorghum [Sorghum bicolor (L.) Moench] production is severely affected by anthracnose disease caused by Colletotrichum sublineolum Henn. New sources of anthracnose resistance should be identified to introgress novel genes into susceptible varieties in resistance breeding programs. The objective of this study was to determine genome-wide association of Diversity Arrays Technology Sequencing (DArTseq) based single nucleotide polymorphisms (SNP) markers and anthracnose resistance genes in diverse sorghum populations for resistance breeding. Three hundred sixty-six sorghum populations were assessed for anthracnose resistance in three seasons in western Ethiopia using artificial inoculation. Data on anthracnose severity and the relative area under the disease progress curve were computed. Furthermore, the test populations were genotyped using SNP markers with DArTseq protocol. Population structure analysis and genome-wide association mapping were undertaken based on 11,643 SNPs with <10% missing data. The evaluated population was grouped into eight distinct genetic clusters. A total of eight significant (P < 0.001) marker-trait associations (MTAs) were detected, explaining 4.86–15.9% of the phenotypic variation for anthracnose resistance. Out of which the four markers were above the cutoff point. The significant MTAs in the assessed sorghum population are useful for marker-assisted selection (MAS) in anthracnose resistance breeding programs and for gene and quantitative trait loci (QTL) mapping.

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Genome-wide association mapping revealed syntenic loci QFhb-4AL and QFhb-5DL for Fusarium head blight resistance in common wheat (Triticum aestivum L.)

10.21203/rs.2.12667/v3 ◽

2019 ◽

Author(s):

Wenjing Hu ◽

Derong Gao ◽

Hongya Wu ◽

Jian Liu ◽

Chunmei Zhang ◽

...

Keyword(s):

Genome Wide Association Study ◽

Resistance Breeding ◽

Snp Markers ◽

Genome Wide Association ◽

Type Ii ◽

Head Blight ◽

Genome Wide ◽

A Genome ◽

Fhb Resistance ◽

Type Ii Resistance

Abstract Background: Fusarium head blight (FHB), primarily caused by Fusarium graminearum, is a major threat to wheat production and food security worldwide. Breeding stably and durably resistant cultivars is the most effective approach for managing and controlling the disease. The success of FHB resistance breeding relies on identification of an effective resistant germplasm. We performed a genome-wide association study (GWAS) using the high-density wheat 90K single nucleotide polymorphism (SNP) assays to better understand the genetic basis of FHB resistance in natural population and identify associated molecular markers. Results: The resistance to FHB fungal spread along the rachis (Type II resistance) was evaluated on 171 wheat cultivars in the 2016-2017 (abbr. as 2017) and 2017-2018 (abbr. as 2018) growing seasons. Using Illumina Infinum iSelect 90K SNP genotyping data, a genome-wide association study (GWAS) identified 26 loci (88 marker-trait associations), which explained 6.65-14.18% of the phenotypic variances. The associated loci distributed across all chromosomes except 2D, 6A, 6D and 7D, with those on chromosomes 1B, 4A, 5D and 7A being detected in both years. New loci for Type II resistance were found on syntenic genomic regions of chromsome 4AL (QFhb-4AL, 621.85-622.24 Mb) and chromosome 5DL (QFhb-5DL, 546.09-547.27 Mb) which showed high collinearity in gene content and order. SNP markers wsnp_JD_c4438_5568170 and wsnp_CAP11_c209_198467 of 5D, reported previously linked to a soil-borne wheat mosaic virus (SBWMV) resistance gene, were also associated with FHB resistance in this study. Conclusion: The syntenic FHB resistant loci and associated SNP markers identified in this study are valuable for FHB resistance breeding via marker-assisted selection.

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Genome-wide association mapping revealed syntenic loci QFhb-4AL and QFhb-5DL for Fusarium head blight resistance in common wheat (Triticum aestivum L.)

10.21203/rs.2.12667/v4 ◽

2019 ◽

Author(s):

Wenjing Hu ◽

Derong Gao ◽

Hongya Wu ◽

Jian Liu ◽

Chunmei Zhang ◽

...

Keyword(s):

Genome Wide Association Study ◽

Resistance Breeding ◽

Snp Markers ◽

Genome Wide Association ◽

Type Ii ◽

Head Blight ◽

Genome Wide ◽

A Genome ◽

Fhb Resistance ◽

Type Ii Resistance

Abstract Background: Fusarium head blight (FHB), primarily caused by Fusarium graminearum, is a major threat to wheat production and food security worldwide. Breeding stably and durably resistant cultivars is the most effective approach for managing and controlling the disease. The success of FHB resistance breeding relies on identification of an effective resistant germplasm. We conducted a genome-wide association study (GWAS) using the high-density wheat 90K single nucleotide polymorphism (SNP) assays to better understand the genetic basis of FHB resistance in natural population and identify associated molecular markers. Results: The resistance to FHB fungal spread along the rachis (Type II resistance) was evaluated on 171 wheat cultivars in the 2016-2017 (abbr. as 2017) and 2017-2018 (abbr. as 2018) growing seasons. Using Illumina Infinum iSelect 90K SNP genotyping data, a genome-wide association study (GWAS) identified 26 loci (88 marker-trait associations), which explained 6.65-14.18% of the phenotypic variances. The associated loci distributed across all chromosomes except 2D, 6A, 6D and 7D, with those on chromosomes 1B, 4A, 5D and 7A being detected in both years. New loci for Type II resistance were found on syntenic genomic regions of chromsome 4AL (QFhb-4AL, 621.85-622.24 Mb) and chromosome 5DL (QFhb-5DL, 546.09-547.27 Mb) which showed high collinearity in gene content and order. SNP markers wsnp_JD_c4438_5568170 and wsnp_CAP11_c209_198467 of 5D, reported previously linked to a soil-borne wheat mosaic virus (SBWMV) resistance gene, were also associated with FHB resistance in this study. Conclusion: The syntenic FHB resistant loci and associated SNP markers identified in this study are valuable for FHB resistance breeding via marker-assisted selection.

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Genome Wide Association Study of Karnal Bunt Resistance in a Wheat Germplasm Collection from Afghanistan

International Journal of Molecular Sciences ◽

10.3390/ijms20133124 ◽

2019 ◽

Vol 20 (13) ◽

pp. 3124 ◽

Cited By ~ 5

Author(s):

Vikas Gupta ◽

Xinyao He ◽

Naresh Kumar ◽

Guillermo Fuentes-Davila ◽

Rajiv K. Sharma ◽

...

Keyword(s):

Association Study ◽

Genome Wide Association Study ◽

Germplasm Collection ◽

Resistance Breeding ◽

Snp Markers ◽

Genome Wide Association ◽

Karnal Bunt ◽

Genome Wide ◽

Genomic Regions ◽

Bunt Resistance

Karnal bunt disease of wheat, caused by the fungus Neovossia indica, is one of the most important challenges to the grain industry as it affects the grain quality and also restricts the international movement of infected grain. It is a seed-, soil- and airborne disease with limited effect of chemical control. Currently, this disease is contained through the deployment of host resistance but further improvement is limited as only a few genotypes have been found to carry partial resistance. To identify genomic regions responsible for resistance in a set of 339 wheat accessions, genome-wide association study (GWAS) was undertaken using the DArTSeq® technology, in which 18 genomic regions for Karnal bunt resistance were identified, explaining 5–20% of the phenotypic variation. The identified quantitative trait loci (QTL) on chromosome 2BL showed consistently significant effects across all four experiments, whereas another QTL on 5BL was significant in three experiments. Additional QTLs were mapped on chromosomes 1DL, 2DL, 4AL, 5AS, 6BL, 6BS, 7BS and 7DL that have not been mapped previously, and on chromosomes 4B, 5AL, 5BL and 6BS, which have been reported in previous studies. Germplasm with less than 1% Karnal bunt infection have been identified and can be used for resistance breeding. The SNP markers linked to the genomic regions conferring resistance to Karnal bunt could be used to improve Karnal bunt resistance through marker-assisted selection.

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Genome-Wide Association Studies Provide Insights into the Genetic Determination of Flower and Leaf Traits of Actinidia eriantha

Frontiers in Plant Science ◽

10.3389/fpls.2021.730890 ◽

2021 ◽

Vol 12 ◽

Author(s):

Guanglian Liao ◽

Min Zhong ◽

Zhiqiang Jiang ◽

Junjie Tao ◽

Dongfeng Jia ◽

...

Keyword(s):

Molecular Breeding ◽

Association Studies ◽

Pollen Viability ◽

Snp Markers ◽

Genome Wide Association ◽

Genome Wide Association Studies ◽

Phylogenetic Tree Analysis ◽

Genetic Determination ◽

Genome Wide ◽

Population Structure Analysis

Kiwifruit (Actinidia eriantha) is a dioecious vine, and the pollen of its male cultivars has a direct effect on the quality of its fruits. In this study, to facilitate molecular breeding and gene identification, we performed genome-wide association studies (GWAS) on 11 traits of flower and leaf. A total of 946,337 highly consistent SNP markers were obtained in the whole genome. Phylogenetic tree analysis and population structure analysis showed that the 143 germplasms can be divided into two groups. The linkage disequilibrium analysis showed that A. eriantha have a relatively fast attenuation rate, and that the average attenuation distance of LD was 0.1–0.3 Kb. The MLM (QK) model was determined as best for correlation analysis, and eight and three SNPs associated with flower- and leaf-related traits were identified, respectively, at 0.01 significance level. However, SNP markers associated with stamen number per flower, pollen viability, total chlorophyll content, and total flavonoid content were not identified at the 0.01 significant level, although it is worth noting that one, one, five, and two SNPs were identified to be associated with these traits at the 0.05 significant level. This study provides insights into the complex flower- and leaf-related biology, and identifies genes controlling important traits in A. eriantha through GWAS, which extends the genetic resources and basis for facilitating molecular breeding in kiwifruits.

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Genome-wide association mapping revealed syntenic loci QFhb-4AL and QFhb-5DL for Fusarium head blight resistance in common wheat (Triticum aestivum L.)

10.21203/rs.2.12667/v1 ◽

2019 ◽

Author(s):

Wenjing Hu ◽

Derong Gao ◽

Hongya Wu ◽

Jian Liu ◽

Chunmei Zhang ◽

...

Keyword(s):

Genome Wide Association Study ◽

Resistance Breeding ◽

Snp Markers ◽

Genome Wide Association ◽

Type Ii ◽

Head Blight ◽

Genome Wide ◽

A Genome ◽

Fhb Resistance ◽

Type Ii Resistance

Abstract Background:Fusarium head blight (FHB), primarily caused by Fusarium graminearum, is a major threat to wheat production and food security worldwide. Breeding stably and durably resistant cultivars is the most effective approach for managing and controlling the disease. The success of FHB resistance breeding relies on identification of an effective resistant germplasm. We performed a genome-wide association study (GWAS) using the high-density wheat 90K single nucleotide polymorphism (SNP) assays to better understand the genetic basis of FHB resistance in natural population and identify associated molecular markers. Results:The resistance to FHB fungal spread along the rachis (Type II resistance) was evaluated on 171 wheat cultivars in the 2016-2017 and 2017-2018 growing seasons. Using Illumina Infinum iSelect 90K SNP genotyping data, a genome-wide association study (GWAS) identified 26 loci(88 marker-trait associations), which explained 6.65-14.18% of the phenotypic variances. The associated loci distributed across all chromosomes except 2D, 6A, 6D and 7D, with those on chromosomes 1B, 4A, 5D and 7A being detected in both years. New loci for Type II resistance were found on syntenic genomic regions of chromsome 4AL (QFhb-4AL, 621.85 - 622.24 Mb) and chromosome 5DL (QFhb-5DL, 546.09 - 547.27 Mb) which showed highly collinarity in gene content and order. SNP markers wsnp_JD_c4438_5568170 and wsnp_CAP11_c209_198467 of 5D, reported previously linked to a soil-borne wheat mosaic virus (SBWMV) resistance gene, were also associated with FHB resistance in this study. Conclusion:The syntenic FHB resistant loci and associated SNP markers identified in this study are valuable for FHB resistance breeding via marker-assisted selection.

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Dissecting Four Correlated Growth Period Traits Using a Genome-Wide Association Study Approach in Soybean

10.21203/rs.3.rs-188488/v1 ◽

2021 ◽

Author(s):

Yinghui Li ◽

Li Yanfei ◽

Hong Huilong ◽

Ma Yansong ◽

Gu Yongzhe ◽

...

Keyword(s):

Association Study ◽

Genome Wide Association Study ◽

Growth Period ◽

Snp Markers ◽

Genome Wide Association ◽

Nucleotide Polymorphisms ◽

Study Approach ◽

Genome Wide ◽

A Genome ◽

Photoperiod Sensitive

Abstract Soybean (Glycine max (L.) Merri) is a short-day, photoperiod-sensitive crop. The vegetative growth period (V), reproductive growth period (R), whole growth period (V + R) and the ratio of growth period structure (R/V) are photoperiod traits critical to adaptability and yield in soybean. To thoroughly dissect the genetic basis of these growth period traits and their correlations, a panel of 277 soybean accessions were genotyped with a single nucleotide polymorphisms (SNPs) chip and phenotyped at three field environments over three years. A genome-wide association study found 29 SNPs on fifteen chromosomes with 33 significant marker-trait associations, eleven, eight, four and ten for V, R, V + R and R/V, respectively. Two SNPs, Map-6077 and − 6502, showed pleiotropy in three and two traits, respectively. Map-6077, associated with V, R, and V + R, was a synonymous SNP of the GmMFT, a member of PEBP family that has been reported to inhibit seed germination and regulate oil content. These results provide candidate SNP markers and genes for further functional experiments to advance molecular marker-assisted breeding.

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The Ficus erecta genome to identify the Ceratocystis canker resistance gene for breeding programs in common fig (F. carica)

10.1101/749788 ◽

2019 ◽

Author(s):

Kenta Shirasawa ◽

Hiroshi Yakushiji ◽

Ryotaro Nishimura ◽

Takeshige Morita ◽

Shota Jikumaru ◽

...

Keyword(s):

Single Molecule ◽

Resistance Breeding ◽

Nucleotide Polymorphisms ◽

Donor Genome ◽

Breeding Programs ◽

Common Fig ◽

Genome Wide ◽

Resistance Trait ◽

Whole Genome Resequencing ◽

Recurrent Backcrossing

AbstractFicus erecta, a wild relative of common fig (F. carica), is a donor of Ceratocystis canker resistance in fig breeding programs. Interspecific hybridization followed by recurrent backcrossing is an effective method to transfer the resistance trait from wild to cultivated fig; however, this is time consuming and labor-intensive for trees, especially for gynodioecious plants such as fig. In this study, genome resources were developed for F. erecta to facilitate fig breeding programs. The genome sequence of F. erecta was determined using single-molecule real-time sequencing technology. The resultant assembly spanned 331.6 Mb with 538 contigs and an N50 length of 1.9 Mb, from which 51,806 high-confidence genes were predicted. Pseudomolecule sequences corresponding to the chromosomes of F. erecta were established with a genetic map based on single nucleotide polymorphisms from double-digest restriction-site associated DNA sequencing. Subsequent linkage analysis and whole genome resequencing identified a candidate gene for the Ceratocystis canker resistance trait. Genome-wide genotyping analysis enabled selection of female lines that possessed resistance and effective elimination of donor genome from progeny. The genome resources provided in this study will accelerate and enhance disease resistance breeding programs in fig.

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Identification of new QTLs for resistance to Plasmodiophora brassicae in Brassica napus using genome wide association mapping

10.21203/rs.2.14300/v1 ◽

2019 ◽

Author(s):

Abdulsalam Dakouri ◽

Mebarek Lamara ◽

Md. Masud Karim ◽

Jinghe Wang ◽

Qilin Chen ◽

...

Keyword(s):

Brassica Napus ◽

Association Mapping ◽

Resistance Genes ◽

Plasmodiophora Brassicae ◽

Snp Markers ◽

Genome Wide Association ◽

Sources Of Resistance ◽

Genome Wide ◽

Population Structure Analysis ◽

A Genome

Abstract Background Clubroot of canola ( Brassica napus ), caused by the obligate pathogen Plasmodiophora brassicae Woronin, is a major disease worldwide. Genetic resistance remains the best strategy to manage this disease. The objective of the study was to identify and map new sources of resistance to clubroot in B. napus using genome-wide association mapping. The reaction of a collection of 177 accessions to four highly virulent pathotypes of P. brassicae was assessed. These pathotypes were selected because they were most recently identified and showed different virulence patterns on the Canadian clubroot differential (CCD) lines. The collection was then genotyped using genotyping by sequencing (GBS) method. Multi-locus mixed linear model (MMLM) was used to perform the association analysis. Results The majority of accessions were highly susceptible (70 –100 DSI), while few individual accessions showed strong resistance (0–20 DSI) to 5X (2 accessions), 2B (7 accessions), 3A (8 accessions) and 3D (15 accessions). In total, 301,753 SNPs were mapped to 19 chromosomes. Population structure analysis indicated that the 177 accessions belong to two major populations. SNPs were associated with resistance to each pathotype using MLMM. In total, 23 significant SNP loci were identified, with 14 SNPs mapped to the A-genome and 9 to the C-genome. The SNPs were associated with resistance to pathotypes 5X (4 SNPs), 2B (9), 3A (5) and 3D (5). A blast search of 2 Mb upstream and downstream identified 61 disease resistance genes, of which 24 belonged to TIR-NBS-LRR proteins and 20 belonged to CC-NBS-LRR proteins. The distance between a SNP locus and the nearest resistance genes ranged from 0.11–1.66 Mb. This indicated that NBS-LRR gene family might have an important role in clubroot resistance in B. napus . Conclusion The resistant B. napus lines and the SNP markers identified in this study can be used for breeding for resistance to clubroot and contribute to understanding the genetic mechanism of resistance to clubroot.

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Genome-wide association mapping revealed syntenic loci QFhb-4AL and QFhb-5DL for Fusarium head blight resistance in common wheat (Triticum aestivum L.)

10.21203/rs.2.12667/v2 ◽

2019 ◽

Author(s):

Wenjing Hu(Former Corresponding Author) ◽

Derong Gao ◽

Hongya Wu ◽

Jian Liu ◽

Chunmei Zhang ◽

...

Keyword(s):

Genome Wide Association Study ◽

Resistance Breeding ◽

Snp Markers ◽

Genome Wide Association ◽

Type Ii ◽

Head Blight ◽

Genome Wide ◽

A Genome ◽

Fhb Resistance ◽

Type Ii Resistance

Abstract Background: Fusarium head blight (FHB), primarily caused by Fusarium graminearum, is a major threat to wheat production and food security worldwide. Breeding stably and durably resistant cultivars is the most effective approach for managing and controlling the disease. The success of FHB resistance breeding relies on identification of effective resistant germplasm. We performed a genome-wide association study (GWAS) using the high-density wheat 90K single nucleotide polymorphism (SNP) assays to better understand the genetic basis of FHB resistance in natural population and identify associated molecular markers. Results: The resistance to FHB fungal spread along the rachis (Type II resistance) was evaluated on 171 wheat cultivars in the 2016-2017 (abbr. as 2017) and 2017-2018 (abbr. as 2018) growing seasons. Using Illumina Infinum iSelect 90K SNP genotyping data, a genome-wide association study (GWAS) identified 26 loci（88 marker-trait associations）, which explained 6.65-14.18% of the phenotypic variances. The associated loci distributed across all chromosomes except 2D, 6A, 6D and 7D, with those on chromosomes 1B, 4A, 5D and 7A being detected in both years. New loci for Type II resistance were found on syntenic genomic regions of chromsome 4AL ( QFhb-4AL , 621.85 Mb - 622.24 Mb) and chromosome 5DL ( QFhb-5DL , 546.09 Mb - 547.27 Mb) which showed highly collinearity in gene content and order. SNP markers wsnp_JD_c4438_5568170 and wsnp_CAP11_c209_198467 of 5D, reported previously linked to a soil-borne wheat mosaic virus (SBWMV) resistance gene, were also associated with FHB resistance in this study. Conclusion: The syntenic FHB resistant loci and associated SNP markers identified in this study are valuable for FHB resistance breeding via marker-assisted selection.

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Comprehensive Genome-Wide Association Analysis Reveals the Genetic Basis of Root System Architecture in Soybean

Frontiers in Plant Science ◽

10.3389/fpls.2020.590740 ◽

2020 ◽

Vol 11 ◽

Author(s):

Waldiodio Seck ◽

Davoud Torkamaneh ◽

François Belzile

Keyword(s):

Root System ◽

System Architecture ◽

Phenotypic Variation ◽

Genetic Basis ◽

Genome Wide Association Study ◽

Primary Root ◽

Root System Architecture ◽

Genome Wide Association ◽

Nucleotide Polymorphisms ◽

Genome Wide

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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