40 Novel Genomic Regions Associated with Igg Antibody Response to PRRSV Vaccination Revealed by Haplotype-based GWAS

2021 ◽  
Vol 99 (Supplement_1) ◽  
pp. 31-32
Author(s):  
Leticia P Sanglard ◽  
Yijian Huang ◽  
Kent A Gray ◽  
Daniel Linhares ◽  
Jack C Dekkers ◽  
...  
Keyword(s):  
Antibody Response ◽  
Candidate Genes ◽  
Genetic Variance ◽  
Genome Wide Association Study ◽  
Chromosome 7 ◽  
Respiratory Syndrome Virus ◽  
Igg Antibody ◽  
Large White ◽  
Genomic Study ◽  
Genomic Regions

Abstract Previous studies on genomics of antibody response, measured as sample-to-positive (S/P) ratio, to Porcine Reproductive and Respiratory Syndrome virus (PRRSV) have reported a major quantitative trait locus (QTL) on the major histocompatibility complex (MHC) on chromosome 7, explaining ~25% of the genetic variance of this trait. S/P ratio following modified live PRRSV vaccination in crossbred commercial gilts has been proposed as genetic indicator for reproductive performance in non-infected purebred sows and PRRSV-vaccinated crossbred sows. This motivated further genomic study for this trait by performing haplotype-based genome-wide association study (GWAS). 906 naïve F1 (Landrace x Large White) had blood samples taken at ~50d after vaccination for measuring PRRSV ELISA S/P ratio and genotyping. Haplotype-based GWAS identified 8 genomic regions on chromosomes 4 (108 Mb), 7 (15, 21, and 24–27 Mb), and 9 (33 Mb) that were associated (q-value < 0.07) with S/P ratio. From those, only the MHC region (chromosome 7; 24 – 26 Mb) had been identified in the SNP based GWAS. The main SNP identified in the SNP based GWAS (H3GA0020505) was not in LD with the haplotype; thus, we added this SNP to the haplotype model. We observed that the haplotype explained more of the genetic variance compared to the H3GA0020505 SNP, indicating that the MHC haplotype is in stronger LD with the QTL than the H3GA0020505 SNP. All the significant regions associated with S/P ratio included immune-related candidate genes, such as SLA-DOB, TAP2, TAPBP, TMIGD3, and ADORA. This study validated the QTL identified on the MHC region, narrowing the search for causal genes in this region, and identified new genomic regions, along with candidate genes associated with S/P ratio. Identifying novel genomic regions provides more resources for marker-assisted selection and genomic prediction of S/P ratio in purebred and commercial pig populations.

scholarly journals Further host-genomic characterization of total antibody response to PRRSV vaccination and its relationship with reproductive performance in commercial sows: genome-wide haplotype and zygosity analyses

2021 ◽  
Vol 53 (1) ◽  
Author(s):  
Leticia P. Sanglard ◽  
Yijian Huang ◽  
Kent A. Gray ◽  
Daniel C. L. Linhares ◽  
Jack C. M. Dekkers ◽  
...  
Keyword(s):  
Antibody Response ◽  
Reproductive Performance ◽  
Genome Wide Association Study ◽  
Reproductive Traits ◽  
Chromosome 7 ◽  
Potential Candidate ◽  
Genome Wide ◽  
Causal Genes ◽  
Immune Related Genes ◽  
Genomic Regions

Abstract Background The possibility of using antibody response (S/P ratio) to PRRSV vaccination measured in crossbred commercial gilts as a genetic indicator for reproductive performance in vaccinated crossbred sows has motivated further studies of the genomic basis of this trait. In this study, we investigated the association of haplotypes and runs of homozygosity (ROH) and heterozygosity (ROHet) with S/P ratio and their impact on reproductive performance. Results There was no association (P-value ≥ 0.18) of S/P ratio with the percentage of ROH or ROHet, or with the percentage of heterozygosity across the whole genome or in the major histocompatibility complex (MHC) region. However, specific ROH and ROHet regions were significantly associated (P-value ≤ 0.01) with S/P ratio on chromosomes 1, 4, 5, 7, 10, 11, 13, and 17 but not (P-value ≥ 0.10) with reproductive performance. With the haplotype-based genome-wide association study (GWAS), additional genomic regions associated with S/P ratio were identified on chromosomes 4, 7, and 9. These regions harbor immune-related genes, such as SLA-DOB, TAP2, TAPBP, TMIGD3, and ADORA. Four haplotypes at the identified region on chromosome 7 were also associated with multiple reproductive traits. A haplotype significantly associated with S/P ratio that is located in the MHC region may be in stronger linkage disequilibrium (LD) with the quantitative trait loci (QTL) than the previously identified single nucleotide polymorphism (SNP) (H3GA0020505) given the larger estimate of genetic variance explained by the haplotype than by the SNP. Conclusions Specific ROH and ROHet regions were significantly associated with S/P ratio. The haplotype-based GWAS identified novel QTL for S/P ratio on chromosomes 4, 7, and 9 and confirmed the presence of at least one QTL in the MHC region. The chromosome 7 region was also associated with reproductive performance. These results narrow the search for causal genes in this region and suggest SLA-DOB and TAP2 as potential candidate genes associated with S/P ratio on chromosome 7. These results provide additional opportunities for marker-assisted selection and genomic selection for S/P ratio as genetic indicator for litter size in commercial pig populations.

scholarly journals Genome-Wide Association Study Using Fix-Length Haplotypes and Network Analysis Revealed New Candidate Genes for Nematode Resistance and Body Weight in Blackface Lambs

2020 ◽  
Vol 20 (2) ◽  
pp. 445-464
Author(s):  
Amir Hossein Khaltabadi Farahani ◽  
Hossein Mohammadi ◽  
Mohammad Hossein Moradi
Keyword(s):  
Body Weight ◽  
Network Analysis ◽  
Candidate Genes ◽  
Genetic Variance ◽  
Genome Wide Association Study ◽  
Nematode Resistance ◽  
Network Analyses ◽  
Frequency Threshold ◽  
Genomic Regions ◽  
Variance Explained

AbstractThe objectives of this study were to identify genomic regions by Bayesian methods (BayesA, BayesB, or BayesN) that fit fixed-length haplotypes or SNPs using GenSel. Covariates for haplo-type alleles of five lengths (125, 250, 500 kb, 1 or 2 Mb) were generated, and rare haplotypes were removed at three thresholds (1, 5, or 10%). Subsequently, we performed gene network analyses to investigate the biological processes shared by genes that were identified for the same across traits. Genotypes at 41,034 SNPs that were common on OvineSNP50 panel were phased for 751 Scottish Blackface (SBF) lambs. This is the first study to quantify the proportion of genetic variance using haplotypes across the whole genome in an SBF population. The genetic variance explained of haplotype-based GWAS was higher than that of SNP-based GWAS in across traits studied. In this population, fitting 500kb haplotypes with a 1% frequency threshold resulted in the highest proportion of genetic variance explained for nematode resistance and fitting 2Mb haplotypes with a 10% frequency threshold improved genetic variance explained for body weight comparable to fitting SNPs by BayesB. Candidate genes, including CXCR4, STAT4, CCL1, CCL2, CCL3, CCL5, CCL8, CCL16, CCL18, CARMIL2, and HSPA14 were identified for nematode resistance and ADH5, PPP3CA, and FABP4 for body weight traits. Network analysis provided annotation results linking to all identified candidate genes. This study supported previous results from GWAS of nematode resistance and body weight and revealed additional regions in the ovine genome associated with these economically important traits. These results suggest that network analysis can provide new information regarding biological mechanisms and genes leading to complex phenotypes, like nematode resistance and body weight of lamb.

scholarly journals Genomics of response to PRRSV in purebred and crossbred sows: antibody response and performance following natural infection versus vaccination

2021 ◽  
Author(s):  
Leticia P Sanglard ◽  
Felipe M W Hickmann ◽  
Yijian Huang ◽  
Kent A Gray ◽  
Daniel C L Linhares ◽  
...  
Keyword(s):  
Antibody Response ◽  
Genetic Correlation ◽  
Reproductive Performance ◽  
Genetic Relationships ◽  
Natural Infection ◽  
Respiratory Syndrome Virus ◽  
Large White ◽  
And Performance ◽  
Genomic Regions ◽  
Indicator Traits

Abstract Antibody response, measured as sample-to-positive (S/P) ratio, to Porcine Reproductive and Respiratory Syndrome virus (PRRSV) following a PRRSV-outbreak (S/POutbreak) in a purebred nucleus and following a PRRSV-vaccination (S/PVx) in commercial crossbred herds have been proposed as genetic indicator traits for improved reproductive performance in PRRSV-infected purebred and PRRSV-vaccinated crossbred sows, respectively. In this study, we investigated the genetic relationships of S/POutbreak and S/PVx with performance at the commercial (vaccinated crossbred sows) and nucleus level (non-infected and PRRSV-infected purebred sows), respectively, and tested the effect of previously identified SNP for these indicator traits. Antibody response was measured on 541 Landrace sows approximately 54 days after the start of a PRRSV outbreak, and on 906 F1 (Landrace x Large White) gilts approximately 50 days after vaccination with a commercial PRRSV vaccine. Reproductive performance was recorded for 711 and 428 Landrace sows before and during the PRRSV outbreak, respectively, and for 811 vaccinated F1 animals. The estimate of the genetic correlation (rg) of S/POutbreak with S/PVx was 0.72±0.18. The estimates of rg of S/POutbreak with reproductive performance in vaccinated crossbred sows were low to moderate, ranging from 0.05±0.23 to 0.30±0.20. The estimate of rg of S/PVx with reproductive performance in non-infected purebred sows was moderate and favorable with number born alive (0.50±0.23) but low (0±0.23 to -0.11±0.23) with piglet mortality traits. The estimates of rg of S/PVx were moderate and negative (-0.38±0.21) with number of mummies in PRRSV-infected purebred sows and low with other traits (-0.30±0.18 to 0.05±0.18). Several significant associations (P0 > 0.90) of previously reported SNP for S/P ratio (ASGA0032063 and H3GA0020505) were identified for S/P ratio and performance in non-infected purebred and PRRSV-exposed purebred and crossbred sows. Genomic regions harboring the major histocompatibility complex class II region significantly contributed to the genetic correlation of antibody response to PRRSV with most of the traits analyzed. These results indicate that selection for antibody response in purebred sows following a PRRSV outbreak in the nucleus and for antibody response to PRRSV vaccination measured in commercial crossbred sows are expected to increase litter size in purebred and commercial sows.

129 Genomic Relationship Between PRRSV Wild-type Infection and PRRSV Vaccination for Antibody Response and Reproductive Performance

2021 ◽  
Vol 99 (Supplement_1) ◽  
pp. 18-18
Author(s):  
Leticia P Sanglard ◽  
Felipe Hickmann ◽  
Yijian Huang ◽  
Kent A Gray ◽  
Daniel Linhares ◽  
...  
Keyword(s):  
Antibody Response ◽  
Reproductive Performance ◽  
Genetic Correlations ◽  
Clinical Signs ◽  
Respiratory Syndrome Virus ◽  
Wild Type ◽  
Large White ◽  
Selection For ◽  
Indicator Trait ◽  
Type Infection

Abstract Immunoglobulin G antibody response, measured as sample-to-positive (S/P) ratio, to Porcine Reproductive and Respiratory Syndrome virus (PRRSV) has been proposed as an indicator trait for improved reproductive performance in PRRSV-infected purebred sows and PRRSV-vaccinated crossbred gilts. In this study, we investigated the genetic correlations (rg) of S/P ratio following a PRRSV outbreak and PRRSV-vaccination with performance in non-exposed and PRRSV-exposed sows. PRRSV outbreak phase was defined based on previously described methodologies after the detection of typical clinical signs of PRRSV infection. 541 Landrace sows had S/P ratio measured at ~54 days after the beginning of the PRRSV outbreak (S/Poutbreak), and 906 Landrace x Large White naïve F1 gilts had S/P ratio measured at ~50 days after vaccination with a commercial modified live PRRSV vaccine (S/PVx). 711 and 428 Landrace sows had reproductive performance recorded before and during the PRRSV outbreak, respectively. 811 vaccinated F1 animals had farrowing performance for up to 3 parities. All animals were genotyped for ~28K SNPs. The estimate of rg of S/Poutbreakwith S/PVx was high (rg±SE = 0.72±0.18). Estimates of rg of S/Poutbreak with reproductive performance in F1 sows were low to moderate, ranging from 0.05±0.23 (number stillborn) to 0.30±0.20 (total number born). Estimates of rg of S/PVxwith reproductive performance in non-infected purebred sows were moderate and favorable with number born alive (0.50±0.23), but low (0 to -0.11±0.23) with litter mortality traits. Estimates of rg of S/PVx were moderate and negative (-0.47±0.18) with the number of mummies in PRRSV-infected purebred sows and low with other traits (-0.29±0.18 for total number born to 0.05±0.18 for number stillborn). These results indicate that selection for antibody response following a PRRSV outbreak collected in purebred sows and to PRRSV vaccination collected in commercial crossbred gilts may increase litter size of non-infected and PRRSV-exposed purebred and commercial crossbred sows.

scholarly journals Genome-Wide Association Study (GWAS) to Identify Salt-Tolerance QTLs Carrying Novel Candidate Genes in Rice During Early Vegetative Stage

Rice ◽  
2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Leila Nayyeripasand ◽  
Ghasem Ali Garoosi ◽  
Asadollah Ahmadikhah
Keyword(s):  
Association Study ◽  
Candidate Gene ◽  
Candidate Genes ◽  
Salinity Tolerance ◽  
Genome Wide Association Study ◽  
Dry Weight ◽  
Genome Wide Association ◽  
Vegetative Stage ◽  
Genome Wide ◽  
Genomic Regions

Abstract Background Rice is considered as a salt-sensitive plant, particularly at early vegetative stage, and its production is suffered from salinity due to expansion of salt affected land in areas under cultivation. Hence, significant increase of rice productivity on salinized lands is really necessary. Today genome-wide association study (GWAS) is a method of choice for fine mapping of QTLs involved in plant responses to abiotic stresses including salinity stress at early vegetative stage. In this study using > 33,000 SNP markers we identified rice genomic regions associated to early stage salinity tolerance. Eight salinity-related traits including shoot length (SL), root length (RL), root dry weight (RDW), root fresh weight (RFW), shoot fresh weight (SFW), shoot dry weight (SDW), relative water content (RWC) and TW, and 4 derived traits including SL-R, RL-R, RDW-R and RFW-R in a diverse panel of rice were evaluated under salinity (100 mM NaCl) and normal conditions in growth chamber. Genome-wide association study (GWAS) was applied based on MLM(+Q + K) model. Results Under stress conditions 151 trait-marker associations were identified that were scattered on 10 chromosomes of rice that arranged in 29 genomic regions. A genomic region on chromosome 1 (11.26 Mbp) was identified which co-located with a known QTL region SalTol1 for salinity tolerance at vegetative stage. A candidate gene (Os01g0304100) was identified in this region which encodes a cation chloride cotransporter. Furthermore, on this chromosome two other candidate genes, Os01g0624700 (24.95 Mbp) and Os01g0812000 (34.51 Mbp), were identified that encode a WRKY transcription factor (WRKY 12) and a transcriptional activator of gibberellin-dependent alpha-amylase expression (GAMyb), respectively. Also, a narrow interval on the same chromosome (40.79–42.98 Mbp) carries 12 candidate genes, some of them were not so far reported for salinity tolerance at seedling stage. Two of more interesting genes are Os01g0966000 and Os01g0963000, encoding a plasma membrane (PM) H+-ATPase and a peroxidase BP1 protein. A candidate gene was identified on chromosome 2 (Os02g0730300 at 30.4 Mbp) encoding a high affinity K+ transporter (HAK). On chromosome 6 a DnaJ-encoding gene and pseudouridine synthase gene were identified. Two novel genes on chromosome 8 including the ABI/VP1 transcription factor and retinoblastoma-related protein (RBR), and 3 novel genes on chromosome 11 including a Lox, F-box and Na+/H+ antiporter, were also identified. Conclusion Known or novel candidate genes in this research were identified that can be used for improvement of salinity tolerance in molecular breeding programmes of rice. Further study and identification of effective genes on salinity tolerance by the use of candidate gene-association analysis can help to precisely uncover the mechanisms of salinity tolerance at molecular level. A time dependent relationship between salt tolerance and expression level of candidate genes could be recognized.

scholarly journals RAPID COMMUNICATION: Multi-breed validation study unraveled genomic regions associated with puberty traits segregating across tropically adapted breeds1

2019 ◽  
Vol 97 (7) ◽  
pp. 3027-3033 ◽  
Author(s):  
Thaise P Melo ◽  
Marina R S Fortes ◽  
Gerardo A Fernandes Junior ◽  
Lucia G Albuquerque ◽  
Roberto Carvalheiro
Keyword(s):  
Candidate Genes ◽  
Genome Wide Association Study ◽  
Meta Analysis ◽  
Reference Population ◽  
High Linkage Disequilibrium ◽  
P Value ◽  
Early Puberty ◽  
Sexual Precocity ◽  
Tropical Conditions ◽  
Genomic Regions

Abstract An efficient strategy to improve QTL detection power is performing across-breed validation studies. Variants segregating across breeds are expected to be in high linkage disequilibrium (LD) with causal mutations affecting economically important traits. The aim of this study was to validate, in a Tropical Composite cattle (TC) population, QTL associations identified for sexual precocity traits in a Nellore and Brahman meta-analysis genome-wide association study. In total, 2,816 TC, 8,001 Nellore, and 2,210 Brahman animals were available for the analysis. For that, genomic regions significantly associated with puberty traits in the meta-analysis study were validated for the following sexual precocity traits in TC: age at first corpus luteum (AGECL), first postpartum anestrus interval (PPAI), and scrotal circumference at 18 months of age (SC). We considered validated QTL those underpinned by significant markers from the Nellore and Brahman meta-analysis (P ≤ 10–4) that were also significant for a TC trait, i.e., presenting a P-value of ≤10–3 for AGECL, PPAI, or SC. We also considered as validated QTL those regions where significant markers in the reference population were at ±250 kb from significant markers in the validation population. Using this criteria, 49 SNP were validated for AGECL, 4 for PPAI, and 14 for SC, from which 5 were in common with AGECL, totaling 62 validated SNP for these traits and 30 candidate genes surrounding them. Considering just candidate genes closest to the top SNP of each chromosome, for AGECL 8 candidate genes were identified: COL8A1, PENK, ENSBTAG00000047425, BPNT1, ADAMTS17, CCHCR1, SUFU, and ENSBTAG00000046374. For PPAI, 3 genes emerged as candidates (PCBP3, KCNK10, and MRPS5), and for SC 8 candidate genes were identified (SNORA70, TRAC, ASS1, BPNT1, LRRK1, PKHD1, PTPRM, and ENSBTAG00000045690). Several candidate regions presented here were previously associated with puberty traits in cattle. The majority of emerging candidate genes are related to biological processes involved in reproductive events, such as maintenance of gestation, and some are known to be expressed in reproductive tissues. Our results suggested that some QTL controlling early puberty seem to be segregating across cattle breeds adapted to tropical conditions.

scholarly journals GWAS Discovery Of Candidate Genes for Yield-Related Traits in Peanut and Support from Earlier QTL Mapping Studies

Genes ◽  
2019 ◽  
Vol 10 (10) ◽  
pp. 803 ◽  
Author(s):  
Wang ◽  
Yan ◽  
Li ◽  
Li ◽  
Zhao ◽  
...  
Keyword(s):  
Qtl Mapping ◽  
Candidate Genes ◽  
Genome Wide Association Study ◽  
Gene Annotation ◽  
Genotyping By Sequencing ◽  
Nucleotide Polymorphisms ◽  
Market Demand ◽  
Oil Crops ◽  
A Genome ◽  
Genomic Regions

Peanut (Arachis hypogaea L.) is one of the most important oil crops worldwide, and its yet increasing market demand may be met by genetic improvement of yield related traits, which may be facilitated by a good understanding of the underlying genetic base of these traits. Here, we have carried out a genome-wide association study (GWAS) with the aim to identify genomic regions and the candidate genes within these regions that may be involved in determining the phenotypic variation at seven yield-related traits in peanut. For the GWAS analyses, 195 peanut accessions were phenotyped and/or genotyped; the latter was done using a genotyping-by-sequencing approach, which produced a total of 13,435 high-quality single nucleotide polymorphisms (SNPs). Analyses of these SNPs show that the analyzed peanut accessions can be approximately grouped into two big groups that, to some extent, agree with the botanical classification of peanut at the subspecies level. By taking this genetic structure as well as the relationships between the analyzed accessions into consideration, our GWAS analyses have identified 93 non-overlapping peak SNPs that are significantly associated with four of the studied traits. Gene annotation of the genome regions surrounding these peak SNPs have found a total of 311 unique candidate genes. Among the 93 yield-related-trait-associated SNP peaks, 12 are found to be co-localized with the quantitative trait loci (QTLs) that were identified by earlier related QTL mapping studies, and these 12 SNP peaks are only related to three traits and are almost all located on chromosomes Arahy.05 and Arahy.16. Gene annotation of these 12 co-localized SNP peaks have found 36 candidates genes, and a close examination of these candidate genes found one very interesting gene (arahy.RI9HIF), the rice homolog of which produces a protein that has been shown to improve rice yield when over-expressed. Further tests of the arahy.RI9HIF gene, as well as other candidate genes especially those within the more confident co-localized genomic regions, may hold the potential for significantly improving peanut yield.

scholarly journals Large-Scale Integration of Meta-QTL and Genome-Wide Association Study Discovers the Genomic Regions and Candidate Genes for Yield and Yield-related Traits in Bread Wheat

2021 ◽  
Author(s):  
Yang Yang ◽  
Amo Aduragbemi ◽  
Di Wei ◽  
Yongmao Chai ◽  
Jie Zheng ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Large Scale ◽  
Genome Wide Association Study ◽  
Expression Patterns ◽  
Wheat Yield ◽  
Natural Populations ◽  
Wheat Breeding ◽  
High Yield ◽  
Photoperiod Response ◽  
Genomic Regions

Abstract Improving yield and yield-related traits are key goals in wheat breeding program. The integration of accumulated wheat genetic resources provides an opportunity to uncover important genomic regions and candidate genes that affect wheat yield. Here, a comprehensive Meta-QTL analysis was conducted on 2230 QTLs of yield-related traits obtained from 119 QTL studies. These QTLs were refined into 145 Meta-QTLs (MQTLs), and 89 MQTLs were verified by GWAS with different natural populations. The average confidence interval (CI) of these MQTLs was 2.92 times less than that of the initial QTLs. Furthermore, 76 core MQTL regions with a physical distance less than 25 Mb were detected. Based on the homology analysis and expression patterns, 237 candidate genes in the MQTLs involved in photoperiod response, grain development, multiple plant growth regulator pathways, carbon and nitrogen metabolism, and spike and flower organ development were determined. A novel candidate gene TaKAO-4A was confirmed to be significantly associated with grain size, and a CAPS marker was developed based on its dominant haplotype. In summary, this study clarified a method based on the integration of Meta-QTL, GWAS and homology comparison to reveal the genomic regions and candidate genes that affect important yield-related traits in wheat. This work will help to lay a foundation for the identification, transfer and aggregation of these important QTLs or candidate genes in wheat high-yield breeding.

scholarly journals Genome-Wide Association Study of Root Mealiness and Other Texture-Associated Traits in Cassava

2021 ◽  
Vol 12 ◽  
Author(s):  
Kelechi Uchendu ◽  
Damian Ndubuisi Njoku ◽  
Agre Paterne ◽  
Ismail Yusuf Rabbi ◽  
Daniel Dzidzienyo ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Genome Wide Association Study ◽  
Genome Wide Association ◽  
Nucleotide Polymorphisms ◽  
Phenotypic Data ◽  
Genome Wide ◽  
A Genome ◽  
Breeding Programmes ◽  
Vegetables And Fruits ◽  
Genomic Regions

Cassava breeders have made significant progress in developing new genotypes with improved agronomic characteristics such as improved root yield and resistance against biotic and abiotic stresses. However, these new and improved cassava (Manihot esculenta Crantz) varieties in cultivation in Nigeria have undergone little or no improvement in their culinary qualities; hence, there is a paucity of genetic information regarding the texture of boiled cassava, particularly with respect to its mealiness, the principal sensory quality attribute of boiled cassava roots. The current study aimed at identifying genomic regions and polymorphisms associated with natural variation for root mealiness and other texture-related attributes of boiled cassava roots, which includes fibre, adhesiveness (ADH), taste, aroma, colour, and firmness. We performed a genome-wide association (GWAS) analysis using phenotypic data from a panel of 142 accessions obtained from the National Root Crops Research Institute (NRCRI), Umudike, Nigeria, and a set of 59,792 high-quality single nucleotide polymorphisms (SNPs) distributed across the cassava genome. Through genome-wide association mapping, we identified 80 SNPs that were significantly associated with root mealiness, fibre, adhesiveness, taste, aroma, colour and firmness on chromosomes 1, 4, 5, 6, 10, 13, 17 and 18. We also identified relevant candidate genes that are co-located with peak SNPs linked to these traits in M. esculenta. A survey of the cassava reference genome v6.1 positioned the SNPs on chromosome 13 in the vicinity of Manes.13G026900, a gene recognized as being responsible for cell adhesion and for the mealiness or crispness of vegetables and fruits, and also known to play an important role in cooked potato texture. This study provides the first insights into understanding the underlying genetic basis of boiled cassava root texture. After validation, the markers and candidate genes identified in this novel work could provide important genomic resources for use in marker-assisted selection (MAS) and genomic selection (GS) to accelerate genetic improvement of root mealiness and other culinary qualities in cassava breeding programmes in West Africa, especially in Nigeria, where the consumption of boiled and pounded cassava is low.

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