Genome-wide association study of cassava brown streak disease resistance in cassava germplasm conserved in South America DOI Creative Commons

Jessica Ospina,

Diana López,

Winnie Gimode

и другие.

Scientific Reports, Год журнала: 2024, Номер 14(1)

Опубликована: Окт. 4, 2024

Cassava (Manihot esculenta Crantz) is a vital carbohydrate source for over 800 million people globally, yet its production in East Africa severely affected by cassava brown streak disease (CBSD). Genebanks, through ex-situ conservation, play pivotal role preserving crop diversity, providing crucial resources breeding resilient and disease-resistant crops. This study genotyped 234 South American accessions conserved at the CIAT genebank, previously phenotyped CBSD resistance an independent group, to perform genome-wide association analysis (GWAS) identify genetic variants associated with resistance. Our GWAS identified 35 single nucleotide polymorphism (SNP) markers distributed across various chromosomes, severity or presence/absence of viral infection. Markers were annotated within near genes functions related pathogen recognition immune response activation. Using SNP candidates, we screened world's largest collection higher frequency favorable genotypes, proposing potential CBSD. results provide insights into genetics highlight importance equip breeders raw materials needed develop new varieties resistant pests diseases.

Язык: Английский

Identification of Genomic Regions for Traits Associated with Flowering in Cassava (Manihot esculenta Crantz) DOI Creative Commons
Julius K. Baguma, Settumba B. Mukasa, Ephraim Nuwamanya

и другие.

Plants, Год журнала: 2024, Номер 13(6), С. 796 - 796

Опубликована: Март 12, 2024

Flowering in cassava (Manihot esculenta Crantz) is crucial for the generation of botanical seed breeding. However, genotypes preferred by most farmers are erect and poor at flowering or never flower. To elucidate genetic basis flowering, 293 diverse accessions were evaluated flowering-associated traits two locations seasons Uganda. Genotyping using Diversity Array Technology Pty Ltd. (DArTseq) platform identified 24,040 single-nucleotide polymorphisms (SNPs) distributed on 18 chromosomes. Population structure analysis principal components (PCs) kinships showed three clusters; first five PCs accounted 49.2% observed variation. Linkage disequilibrium (LD) estimation averaged 0.32 a distance ~2850 kb (kilo base pairs). Polymorphism information content (PIC) minor allele frequency (MAF) 0.25 0.23, respectively. A genome-wide association study (GWAS) uncovered 53 significant marker–trait associations (MTAs) with involving 27 loci. Two loci, SNPs S5_29309724 S15_11747301, associated all traits. Using Phenotype_Variance_Explained (PVE) ≥ 5%, 44 candidate genes peak SNP sites located within 50 upstream downstream, branching Eight genes, orthologous to Arabidopsis other plant species, had known functional annotations related e.g., eukaryotic translation initiation factor myb family transcription factor. This genomic regions cassava, can be useful marker-assisted selection overcome hybridization challenges, like unsynchronized gene validation.

Язык: Английский

Процитировано

3
Genetic complexity of cassava brown streak disease: insights from qPCR-based viral titer analysis and genome-wide association studies DOI Creative Commons

Leah Nandudu,

Samar Sheat, Stephan Winter

и другие.

Frontiers in Plant Science, Год журнала: 2024, Номер 15

Опубликована: Март 13, 2024

Cassava, a vital global food source, faces threat from Cassava Brown Streak Disease (CBSD). CBSD results two viruses: brown streak virus (CBSV) and Ugandan cassava (UCBSV). These viruses frequently pose challenges to the traditional symptom-based 1-5 phenotyping method due its limitations in terms of accuracy objectivity. Quantitative polymerase chain reaction (qPCR) offers precise quantification, although high costs hinder widespread adoption. In this research, we utilized qPCR measure viral titer/load CBSV UCBSV. The objectives were evaluate titer variability within Cycle 2 (C2) population different environments, establish connections between titers severity scores scoring method, perform Genome-Wide Association Studies (GWAS) identify genomic regions associated with UCBSV titers, investigate functional annotated genes. demonstrated significantly higher prevalence (50.2%) clones compared (12.9%) mixed infections some cases. Genotypic effects, particularly concerning UCBSV, significant, genotype-by-environment effects primarily influencing titer. GWAS identified titers. Twenty-one SNP markers on chromosomes 10, 13, 17, 18 exhibited significant associations titer, collectively explaining 43.14% phenotypic variation. Additionally, 25 1, 2, 4, 5, 8, 11, 12, 16, explained 70.71% No shared Gene ontology analysis also revealed diverse gene functions, especially transport catalytic activities. findings enhance our understanding prevalence, genetics, molecular functions plants, offering valuable insights for targeted breeding strategies.

Язык: Английский

Процитировано

1
Genome‐wide association study for yield and quality of granulated cassava processed product DOI Creative Commons
Cynthia Idhigu Aghogho, Siraj Ismail Kayondo, John Saviour Yaw Eleblu

и другие.

The Plant Genome, Год журнала: 2024, Номер 17(2)

Опубликована: Июнь 1, 2024

The starchy storage roots of cassava are commonly processed into a variety products, including granulated products (gari). commercial value depends on the yield and quality directly influencing acceptance new varieties by farmers, processors, consumers. This study aims to estimate genetic advance through phenotypic selection identify genomic regions associated candidate genes linked with gari quality. Higher single nucleotide polymorphism (SNP)-based heritability estimates compared broad-sense were observed for most traits highlighting influence factors variation. Using genome-wide association analysis 188 clones, genotyped using 53,150 SNPs, nine SNPs located seven chromosomes significantly peel loss, yield, color parameters eba, bulk density, swelling index, textural properties eba. Future research will focus validating understanding functions identified their traits.

Язык: Английский

Процитировано

1
Identification of Genomic Regions Associated with Flowering Traits in Cassava (<em>Manihot esculenta </em>Crantz) DOI Open Access
Julius K. Baguma,

Ssettumba B. Mukasa,

Ephraim Nuwamanya

и другие.

Опубликована: Дек. 4, 2023

Flowering in cassava is crucial for generation of botanical seed breeding. However, most farmer preferred genotypes are poor at flowering, exhibit great disparity time and amount flowering or never flower. To elucidate the genetic basis such a behaviour, 293 diverse accessions were evaluated traits under two locations seasons Uganda. Genotyping by Diversity Array Technology Pty Ltd. (DArTseq) platform identified 24,040 single-nucleotide polymorphisms (SNPs) distributed on 18 chromosomes. Population structure analysis using principal components (PC) kinships showed clustering, first five PCs accounted 49.2% observed variation. Linkage disequilibrium (LD) estimation was averagely 0.32 distance ~2850kb (kilo base pairs). Polymorphism information content (PIC) minor allele frequency (MAF) 0.25 0.23, respectively. Genome-wide association study (GWAS) uncovered 53 significant marker-trait associations (MTA) with involving 27 loci. Two loci, SNPs S5_29309724 S15_11747301 associated all traits. Using Phenotype_Variance_Explained (PVE) ≥ 5%, 37 candidate genes peak SNP sites located within 50kb upstream downstream, branching Eight genes, orthologous to Arabidopsis other plant species, had known functional annotations related e.g. eukaryotic translation initiation factor myb family transcription factor. This genomic regions cassava, could be useful marker-assisted selection overcome hybridization challenges like unsynchronized gene validation.

Язык: Английский

Процитировано

1
Genetic analysis of cassava brown streak disease root necrosis using image analysis and genome-wide association studies DOI Creative Commons

Leah Nandudu,

Christopher Strock, Alex C. Ogbonna

и другие.

Frontiers in Plant Science, Год журнала: 2024, Номер 15

Опубликована: Март 18, 2024

Cassava brown streak disease (CBSD) poses a substantial threat to food security. To address this challenge, we used PlantCV extract CBSD root necrosis image traits from 320 clones, with an aim of identifying genomic regions through genome-wide association studies (GWAS) and candidate genes. Results revealed strong correlations among certain traits, such as necrotic area fraction width fraction, well between the convex hull percentage necrosis. Low were observed scores obtained 1-5 scoring method all traits. Broad-sense heritability estimates ranged low moderate, highest estimate 0.42 for necrosis, while narrow-sense consistently remained low, ranging 0.03 0.22. Leveraging data 30,750 SNPs DArT genotyping, eight on chromosomes 1, 7, 11 identified associated both ellipse eccentricity GWAS. Candidate gene analysis in 172.2kb region chromosome 1 24 potential genes diverse functions, including ubiquitin-protein ligase, DNA-binding transcription factors, RNA metabolism protein, others. Despite our initial expectation that objectivity would yield better stronger associations than method, results unexpectedly lower. Further research is needed comprehensively understand genetic basis these their relevance cassava breeding management.

Язык: Английский

Процитировано

0
Genome-wide association study of cassava brown streak disease resistance in cassava germplasm conserved in South America DOI Creative Commons

Jessica Ospina,

Diana López,

Winnie Gimode

и другие.

Scientific Reports, Год журнала: 2024, Номер 14(1)

Опубликована: Окт. 4, 2024

Cassava (Manihot esculenta Crantz) is a vital carbohydrate source for over 800 million people globally, yet its production in East Africa severely affected by cassava brown streak disease (CBSD). Genebanks, through ex-situ conservation, play pivotal role preserving crop diversity, providing crucial resources breeding resilient and disease-resistant crops. This study genotyped 234 South American accessions conserved at the CIAT genebank, previously phenotyped CBSD resistance an independent group, to perform genome-wide association analysis (GWAS) identify genetic variants associated with resistance. Our GWAS identified 35 single nucleotide polymorphism (SNP) markers distributed across various chromosomes, severity or presence/absence of viral infection. Markers were annotated within near genes functions related pathogen recognition immune response activation. Using SNP candidates, we screened world's largest collection higher frequency favorable genotypes, proposing potential CBSD. results provide insights into genetics highlight importance equip breeders raw materials needed develop new varieties resistant pests diseases.

Язык: Английский

Процитировано

0