Major Gene Effect Research Articles

Genome-Wide Association Study of Pericarp Color in Rice Using Different Germplasm and Phenotyping Methods Reveals Different Genetic Architectures.

Pericarp colors (PC) in rice are determined by the types and content of flavonoids in the pericarp. The flavonoid compounds have strong antioxidant activities and are beneficial to human health. However, the genetic basis of PC in rice is still not well-understood. In this study, a genome-wide association study (GWAS) of PC was performed in a diverse rice collection consisting of 442 accessions using different phenotyping methods in two locations over 2 years. In the whole population consisting of white and colored pericarp rice, a total of 11 quantitative trait loci (QTLs) were identified using two phenotyping methods. Among these QTLs, nine were identified using the phenotypes represented by the presence and absence of pigmentation in pericarp, while 10 were identified using phenotypes of the degree of PC (DPC), in which eight are common QTLs identified using the two phenotyping methods. Using colored rice accessions and phenotypes based on DPC, four QTLs were identified, and they were totally different from the QTLs identified using the whole population, suggesting the masking effects of major genes on minor genes. Compared with the previous studies, 10 out of the 15 QTLs are first reported in this study. Based on the differential expression analysis of the predicted genes within the QTL region by both RNA-seq and real-time PCR (RT-PCR) and the gene functions in previous studies, LOC_Os01g49830, encoding a RAV transcription factor was considered as the candidate gene underlying qPC-1, a novel QTL with a large effect in this study. Our results provide a new insight into the genetic basis of PC in rice and contribute to developing the value-added rice with optimized flavonoid content through molecular breeding.

Genetic variation in skin traits in New Zealand lambs.

BACKGROUNDThis study explored the genetic variability in the New Zealand sheep population for economically important skin traits. Skins were collected at slaughter from two progeny test flocks, resulting in 725 skins evaluated for grain strain, flatness, crust leather strength and overall suitability for shoe leather. DNA profiles collected from skins post‐slaughter were matched to individual animals using previously collected high‐density genotypes.RESULTSConsiderable phenotypic variation for skin traits was observed, with around 40% of the skins being identified as suitable for high‐value shoe leather production. Several key traits associated with leather production, including flatness, tear strength, grain strength and grain strain were found to be moderate to highly heritable (h 2 = 0.28–0.82).There were no major significant genome‐wide association study (GWAS) peaks associated with many of the traits examined, however, one single‐nucleotide polymorphism (SNP) reached significance for the flatness of the skin over the hindquarters.CONCLUSIONThis research confirms that suitable lamb skins can be bred for use as high‐value shoe leather. While moderately to highly heritable, skin traits in New Zealand lambs appear to be polygenic with no genes of major effect underlaying the traits of interest. Given the complex nature of these traits, the identification and selection of animals with higher‐value skins may be enabled by geomic selection. © 2022 The Authors. Journal of The Science of Food and Agriculture published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

A Calmodulin-Like Gene (GbCML7) for Fiber Strength and Yield Improvement Identified by Resequencing Core Accessions of a Pedigree in Gossypium barbadense.

Sea Island cotton (Gossypium barbadense) is world-renowned for its superior natural fiber. Although fiber strength is one of the most important fiber quality traits, genes contributing to fiber strength are poorly understood. Production of sea island cotton also is inextricably linked to improving its relatively low yield, thus enhancing the importance of joint improvement of both fiber quality and yield. We used genomic variation to uncover the genetic evidence of trait improvement resulting from pedigree breeding of Sea Island cotton. This pedigree was aimed at improving fiber strength and yielded an elite cultivar, XH35. Using a combination of genome-wide association study (GWAS) and selection screens, we detected 82 putative fiber-strength-related genes. Expression analysis confirmed a calmodulin-like gene, GbCML7, which enhanced fiber strength in a specific haplotype. This gene is a major-effect gene, which interacts with a minor-effect gene, GbTUA3, facilitating the enhancement of fiber strength in a synergistic fashion. Moreover, GbCML7 participates in the cooperative improvement of fiber strength, fiber length, and fiber uniformity, though a slight compromise exists between the first two of these traits and the latter. Importantly, GbCML7 is shown to boost yield in some backgrounds by increasing multiple yield components to varying degrees, especially boll number. Our work provides valuable genomic evidence and a key genetic factor for the joint improvement of fiber quality and yield in Sea Island cotton.

Basis of Inheritance in Humans.

In humans, traits and diseases are inherited primarily by complex or multifactorial modes. These imply that contributions come from more than one gene, and these can be influenced by the environment. They are the mechanisms that underlie inheritance of dental caries, erosive tooth wear, and amelogenesis. Major gene effects (monogenic or Mendelian inheritance) and chromosomal abnormalities explain the scenarios that do not fit well with complex or multifactorial inheritance. Furthermore, there are numerous non-traditional modes of inheritance. These are all exceptions of the most common complex modes of inheritance, and their understanding is important for a number of relatively rare scenarios in humans. In this chapter, these modes of inheritance are presented, and some rare conditions are explored to highlight the relevance of studying rare diseases for the understanding of more common diseases that affect populations, using dental caries as a model.

Herança do teor de betacaroteno em melão

Abstract The objective of this work was to determine the inheritance of beta-carotene content in melon (Cucumis melo). The AC-16 accession (Cucumis melo subsp. melo var. acidulus) – with a low beta-carotene content and white mesocarp – was crossed with the Vedrantais cultivar (C. melo subsp. melo var. cantalupensis) – with a high beta-carotene content and salmon colored mesocarp –, to obtain the F1, F2, BC1, and BC2 generations. The AC-16 and 'Vedrantais' parents, the F1 and F2 generations, and the BC1 and BC2 backcrosses of each parent were evaluated. The quantification of beta-carotene was carried out in a high-performance liquid chromatography system. Mean components related to the additive and dominance effects, additive and dominance variances, and heritability were estimated. The beta-carotene content was high in 'Vedrantais' (17.78 µg g-1) and low in AC-16 (0.34 µg g-1). The following results were observed: additive and dominance effects on the genetic control of the character, incomplete character dominance, estimated number of loci close to two, greater variance for segregating populations (F2 and backcrosses), and heritability values in the broad (87.75%) and narrow (64.19%) senses. The beta-carotene content in melon is controlled by a major effect gene, with additive and dominance effects associated with polygenes with additive effects.

A genome variation map provides insights into the genetics of walnut adaptation and agronomic traits

BackgroundCommon walnut (Juglans regia L.) is one of the top four most consumed nuts in the world due to its health benefits and pleasant taste. Despite its economic importance, the evolutionary history and genetic control of its adaptation and agronomic traits remain largely unexplored.ResultsWe report a comprehensive walnut genomic variation map based on whole-genome resequencing of 815 walnut accessions. Evolutionary analyses suggest that Chinese J. regia diverged from J. sigillata with extensive hybridizations after the split of the two species. In contrast to annual crops, the genetic diversity and heterozygous deleterious mutations of Chinese common walnut trees have continued to increase during the improvement process. Selective sweep analyses identify 902 genes uniquely selected in the improved common walnut compared to its progenitor population. Five major-effect loci are identified to be involved in walnut adaptations to temperature, precipitation, and altitude. Genome-wide association studies reveal 27 genomic loci responsible for 18 important agronomic traits, among which JrFAD2 and JrANR are the potentially major-effect causative genes controlling linoleic acid content and color of the endopleura of the nut, respectively.ConclusionsThe largest genomic resource for walnuts to date has been generated and explored in this study, unveiling their evolutionary history and cracking the genetic code for agronomic traits and environmental adaptation of this economically crucial crop tree.

EPAS1 (Endothelial PAS Domain Protein 1) Orchestrates Transactivation of Endothelial ICAM1 (Intercellular Adhesion Molecule 1) by Small Nucleolar RNA Host Gene 5 (SNHG5) to Promote Hypoxic Pulmonary Hypertension.

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Fur colour in the Arctic fox: genetic architecture and consequences for fitness.

Genome-wide association studies provide good opportunities for studying the genetic basis of adaptive traits in wild populations. Yet, previous studies often failed to identify major effect genes. In this study, we used high-density single nucleotide polymorphism and individual fitness data from a wild non-model species. Using a whole-genome approach, we identified the MC1R gene as the sole causal gene underlying Arctic fox Vulpes lagopus fur colour. Further, we showed the adaptive importance of fur colour genotypes through measures of fitness that link ecological and evolutionary processes. We found a tendency for blue foxes that are heterozygous at the fur colour locus to have higher fitness than homozygous white foxes. The effect of genotype on fitness was independent of winter duration but varied with prey availability, with the strongest effect in years of increasing rodent populations. MC1R is located in a genomic region with high gene density, and we discuss the potential for indirect selection through linkage and pleiotropy. Our study shows that whole-genome analyses can be successfully applied to wild species and identify major effect genes underlying adaptive traits. Furthermore, we show how this approach can be used to identify knowledge gaps in our understanding of interactions between ecology and evolution.

Of bars and stripes: A Malawi cichlid hybrid cross provides insights into genetic modularity and evolution of modifier loci underlying colour pattern diversification.

Understanding the origins of phenotypic diversity among closely related species remains an important largely unsolved question in evolutionary biology. With over 800species, Lake Malawi haplochromine cichlid fishes are a prominent example of extremely fast evolution of diversity including variation in colouration. Previously, a single major effect gene, agrp2 (asip2b), has been linked to evolutionary losses and gains of horizontal stripe patterns in cichlids, but it remains unknown what causes more fine-scale variation in the number and continuity of the stripes. Also, the genetic basis of the most common colour pattern in African cichlids, vertical bars, and potential interactions between the two colour patterns remain unknown. Based on a hybrid cross of the horizontally striped Lake Malawi cichlid Pseudotropheus cyaneorhabdos and the vertically barred species Chindongo demasoni we investigated the genetic basis of both colour patterns. The distribution of phenotypes in the F2 generation of the cross indicates that horizontal stripes and vertical bars are independently inherited patterns that are caused by two sets of genetic modules. While horizontal stripes are largely controlled by few major effect loci, vertical bars are a highly polygenic trait. Horizontal stripes show substantial variation in the F2 generation that, interestingly, resemble naturally occurring phenotypes found in other Lake Malawi cichlid species. Quantitative trait loci (QTL) mapping of this cross reveals known (agrp2) and unknown loci underlying horizontal stripe patterns. These findings provide novel insights into the incremental fine-tuning of an adaptive trait that diversified through the evolution of additional modifier loci.

A Major Effect Gene Controlling Development and Pathogenicity in Botrytis cinerea Identified Through Genetic Analysis of Natural Mycelial Non-pathogenic Isolates.

Botrytis cinerea is a necrotrophic plant pathogenic fungus with a wide host range. Its natural populations are phenotypically and genetically very diverse. A survey of B. cinerea isolates causing gray mold in the vineyards of Castilla y León, Spain, was carried out and as a result eight non-pathogenic natural variants were identified. Phenotypically these isolates belong to two groups. The first group consists of seven isolates displaying a characteristic mycelial morphotype, which do not sporulate and is unable to produce sclerotia. The second group includes one isolate, which sporulates profusely and does not produce sclerotia. All of them are unresponsive to light. Crosses between a representative mycelial non-pathogenic isolate and a highly aggressive field isolate revealed that the phenotypic differences regarding pathogenicity, sporulation and production of sclerotia cosegregated in the progeny and are determined by a single genetic locus. By applying a bulked segregant analysis strategy based on the comparison of the two parental genomes the locus was mapped to a 110 kb region in chromosome 4. Subcloning and transformation experiments revealed that the polymorphism is an SNP affecting gene Bcin04g03490 in the reference genome of B. cinerea. Genetic complementation analysis and sequencing of the Bcin04g03490 alleles demonstrated that the mutations in the mycelial isolates are allelic and informed about the nature of the alterations causing the phenotypes observed. Integration of the allele of the pathogenic isolate into the non-pathogenic isolate fully restored the ability to infect, to sporulate and to produce sclerotia. Therefore, it is concluded that a major effect gene controlling differentiation and developmental processes as well as pathogenicity has been identified in B. cinerea. It encodes a protein with a GAL4-like Zn(II)2Cys6 binuclear cluster DNA binding domain and an acetyltransferase domain, suggesting a role in regulation of gene expression through a mechanism involving acetylation of specific substrates.

Identification of Major Loci and Candidate Genes for Meat Production-Related Traits in Broilers

BackgroundCarcass traits are crucial characteristics of broilers. However, the underlying genetic mechanisms are not well understood. In the current study, significant loci and major-effect candidate genes affecting nine carcass traits related to meat production were analyzed in 873 purebred broilers using an imputation-based genome-wide association study.ResultsThe heritability estimates of nine carcass traits, including carcass weight, thigh muscle weight, and thigh muscle percentage, were moderate to high and ranged from 0.21 to 0.39. Twelve genome-wide significant SNPs and 118 suggestively significant SNPs of 546,656 autosomal variants were associated with carcass traits. All SNPs for six weight traits (body weight at 42 days of age, carcass weight, eviscerated weight, whole thigh weight, thigh weight, and thigh muscle weight) were clustered around the 24.08 Kb region (GGA24: 5.73–5.75 Mb) and contained only one candidate gene (DRD2). The most significant SNP, rs15226023, accounted for 4.85–7.71% of the estimated genetic variance of the six weight traits. The remaining SNPs for carcass composition traits (whole thigh percentage and thigh percentage) were clustered around the 42.52 Kb region (GGA3: 53.03–53.08 Mb) and contained only one candidate gene (ADGRG6). The most significant SNP in this region, rs13571431, accounted for 11.89–13.56% of the estimated genetic variance of two carcass composition traits. Some degree of genetic differentiation in ADGRG6 between large and small breeds was observed.ConclusionWe identified one 24.08 Kb region for weight traits and one 42.52 Kb region for thigh-related carcass traits. DRD2 was the major-effect candidate gene for weight traits, and ADGRG6 was the major-effect candidate gene for carcass composition traits. Our results supply essential information for causative mutation identification of carcass traits in broilers.

Complex pleiotropic genetic architecture of evolved heat stress and oxidative stress resistance in the nematode Caenorhabditis remanei.

The adaptation of complex organisms to changing environments has been a central question in evolutionary quantitative genetics since its inception. The structure of the genotype–phenotype maps is critical because pleiotropic effects can generate widespread correlated responses to selection and potentially restrict the extent of evolutionary change. In this study, we use experimental evolution to dissect the genetic architecture of natural variation for acute heat stress and oxidative stress response in the nematode Caenorhabiditis remanei. Previous work in the classic model nematode Caenorhabiditis elegans has found that abiotic stress response is controlled by a handful of genes of major effect and that mutations in any one of these genes can have widespread pleiotropic effects on multiple stress response traits. Here, we find that acute heat stress response and acute oxidative response in C. remanei are polygenic, complex traits, with hundreds of genomic regions responding to selection. In contrast to expectation from mutation studies, we find that evolved acute heat stress and acute oxidative stress response for the most part display independent genetic bases. This lack of correlation is reflected at the levels of phenotype, gene expression, and in the genomic response to selection. Thus, while these findings support the general view that rapid adaptation can be generated by changes at hundreds to thousands of sites in the genome, the architecture of segregating variation is likely to be determined by the pleiotropic structure of the underlying genetic networks.

DHD4, a CONSTANS-like family transcription factor, delays heading date by affecting the formation of the FAC complex in rice

Heading date (or flowering time) is one of the most important agronomic traits in rice, influencing its regional adaptability and crop yield. Many major-effect genes for rice heading date have been identified, but in practice they are difficult to be used for rice molecular breeding because of their dramatic effects on heading date. Genes with minor effects on heading date, which are more desirable for fine-tuning flowering time without significant yield penalty, were seldom reported. In this study, we identified a new minor-effect heading date repressor, Delayed Heading Date 4 (DHD4). The dhd4 mutant shows a slightly earlier flowering phenotype without a notable yield penalty compared with wild-type plants under natural long-day conditions. DHD4 encodes a CONSTANS-like transcription factor localized in the nucleus. Molecular, biochemical, and genetic assays show that DHD4 can compete with 14-3-3 to interact with OsFD1, thus affecting the formation of the Hd3a-14-3-3-OsFD1 tri-protein FAC complex, resulting in reduced expression of OsMADS14 and OsMADS15, and ultimately delaying flowering. Taken together, these results shed new light on the regulation of flowering time in rice and provide a promising target for fine-tuning flowering time to improve the regional adaptability of rice.

Marker associations for fusiform rust resistance in a clonal population of loblolly pine (Pinus taeda, L.)

Fusiform rust resistance in loblolly pine, Pinus taeda L., is comprised of both polygenic and major gene effects. In this study, we applied a Bayesian approach to test for single nucleotide polymorphisms (SNPs) associated with resistance to fusiform rust, which is caused by Cronartium quercuum (Berk.) Miyabe ex Shirai f.sp. fusiforme. A population of 3810 clonal varieties from 100 full-sib families was produced through somatic embryogenesis and planted in replicated field experiments in the Southeastern United States. Rust phenotypes were measured after 6 growing seasons, and each of 863 clones from 35 full-sib families was genotyped with 3340 SNPs. We identified five associated SNPs with posterior probabilities of inclusion above 0.4 in the clonal population using a BayesCπ model. A second experiment was conducted with one of the identified SNPs (SNP2374) using seedlings from 2 full-sib families that were included in the first experiment. Resistant genotypes exhibited an overall infection rate of 11% compared to the susceptible genotype which had 57% infection. Using one of the full-sib families, we were able to map SNP2374 (CL1208Contig1-03-75) to linkage group 7. Confirmation of the SNP2374 association with rust resistance demonstrates the potential for selecting and screening genotypes to further reduce disease incidence in forest plantations of loblolly pine.

Genetics of Quality Attributes and Powdery Mildew Severity in Garden Pea (Pisum sativum Var. Hortense L.) under Sub Temperate Conditions of North-Western Himalayas

Background: The choice of appropriate breeding method for improvement of traits depends largely on gene action. Hence, an understanding of the inheritance of quantitative traits is essential to develop an efficient breeding strategy.Methods: Twelve generations of three inter-varietal crosses involving four diverse parents of garden pea were studied for biochemical traits and powdery mildew disease severity to analyze the nature of gene effects by using generation mean anaylsis.Result: Duplicate type of epistasis was observed for protein content in all or one or other crosses. In most cases, the presences of linkage among interacting genes or higher order interactions at several loci were involved. Non-fixable gene effects were many times higher than fixable one in all the crosses indicating a major role non-additive gene effects in the inheritance of these traits. The type of gene effects along with presence of non-allelic interactions suggested the adoption of population improvement methods to break undesirable linkages through recombination. The other alternative can be to defer selection in the later generations by advancing segregating populations through bulk pedigree or SSD methods with one or two inter-matings like recurrent selection. Based on pod characteristics and powdery mildew disease severity203 single plant progenies were isolated over the generations of three crosses along with bulk seed following SSD and bulk method to isolate transgressive segregants.

Improving Seed Retention and Germination Characteristics of North American Basin Wildrye by Marker-Assisted Gene Introgression

Basin wildrye [Leymus cinereus (Scribn. and Merr.) Á. Löve] and creeping wildrye [Leymus triticoides (Buckley) Pilg.] are native perennial grasses cultivated for seed used for fire rehabilitation and revegetation in western North America. Although L. cinereus produces large spike inflorescences with many seeds, it is prone to seed shattering. Seed can be harvested before shattering, but often displays poor germination and seedling vigor. Conversely, L. triticoides has fewer seeds per spike, but relatively strong seed retention. Both species are allotetraploid (2n = 4x = 28) and form fertile hybrids used for breeding and genetic research. A dominant, major-effect seed-shattering gene (SH6) from L. cinereus was previously identified in an L. triticoides backcross population. In this study, a DNA marker was used to select the recessive L. triticoides seed-retention allele (sh6) in cycle six (C6) of a L. cinereus × L. triticoides breeding population and evaluate gene × harvest date effects on seed yield and germination characteristics in a full-sib family derived from homozygous (sh6/sh6) and heterozygous (SH6/sh6) C6 parents. Although seed yields of shattering genotypes were 19.4% greater than non-shattering genotypes on the first harvest dates, yields of non-shattering genotypes were 167% greater on the last harvest dates. Seed harvested on the last harvest date reached 50% germination 4.2 days (26.4%) earlier and displayed 20.5% higher upper percentage germination limits than seed harvested on the first harvest date. Results indicate that the sh6 seed-retention gene will improve basin wildrye seed retention and indirectly improve seed germination by enabling later harvest dates.

A Meta-Analysis of Quantitative Trait Loci Associated with Multiple Disease Resistance in Rice (Oryza sativa L.)

Rice blast, sheath blight and bacterial leaf blight are major rice diseases found worldwide. The development of resistant cultivars is generally perceived as the most effective way to combat these diseases. Plant disease resistance is a polygenic trait where a combinatorial effect of major and minor genes affects this trait. To locate the source of this trait, various quantitative trait loci (QTL) mapping studies have been performed in the past two decades. However, investigating the congruency between the reported QTL is a daunting task due to the heterogeneity amongst the QTLs studied. Hence, the aim of our study is to integrate the reported QTLs for resistance against rice blast, sheath blight and bacterial leaf blight and objectively analyze and consolidate the location of QTL clusters in the chromosomes, reducing the QTL intervals and thus identifying candidate genes within the selected meta-QTL. A total of twenty-seven studies for resistance QTLs to rice blast (8), sheath blight (15) and bacterial leaf blight (4) was compiled for QTL projection and analyses. Cumulatively, 333 QTLs associated with rice blast (114), sheath blight (151) and bacterial leaf blight (68) resistance were compiled, where 303 QTLs could be projected onto a consensus map saturated with 7633 loci. Meta-QTL analysis on 294 QTLs yielded 48 meta-QTLs, where QTLs with membership probability lower than 60% were excluded, reducing the number of QTLs within the meta-QTL to 274. Further, three meta-QTL regions (MQTL2.5, MQTL8.1 and MQTL9.1) were selected for functional analysis on the basis that MQTL2.5 harbors the highest number of QTLs; meanwhile, MQTL8.1 and MQTL9.1 have QTLs associated with all three diseases mentioned above. The functional analysis allows for determination of enriched gene ontology and resistance gene analogs (RGAs) and other defense-related genes. To summarize, MQTL2.5, MQTL8.1 and MQTL9.1 have a considerable number of R-genes that account for 10.21%, 4.08% and 6.42% of the total genes found in these meta-QTLs, respectively. Defense genes constitute around 3.70%, 8.16% and 6.42% of the total number of genes in MQTL2.5, MQTL8.1 and MQTL9.1, respectively. This frequency is higher than the total frequency of defense genes in the rice genome, which is 0.0096% (167 defense genes/17,272 total genes). The integration of the QTLs facilitates the identification of QTL hotspots for rice blast, sheath blight and bacterial blight resistance with reduced intervals, which helps to reduce linkage drag in breeding. The candidate genes within the promising regions could be utilized for improvement through genetical engineering.

Comparing Genomic Signatures of Selection Between the Abbassa Strain and Eight Wild Populations of Nile Tilapia (Oreochromis niloticus) in Egypt.

Domestication to captive rearing conditions, along with targeted selective breeding have genetic consequences that vary from those in wild environments. Nile tilapia (Oreochromis niloticus) is one of the most translocated and farmed aquaculture species globally, farmed throughout Asia, North and South America, and its African native range. In Egypt, a breeding program established the Abbassa Strain of Nile tilapia (AS) in 2002 based on local broodstock sourced from the Nile River. The AS has been intensively selected for growth and has gone through genetic bottlenecks which have likely shifted levels and composition of genetic diversity within the strain. Consequently, there are questions on the possible genetic impact AS escapees may have on endemic populations of Nile tilapia. However, to date there have been no genetic studies comparing genetic changes in the domesticated AS to local wild populations. This study used 9,827 genome-wide SNPs to investigate population genetic structure and signatures of selection in the AS (generations 9–11) and eight wild Nile tilapia populations from Egypt. SNP analyses identified two major genetic clusters (captive and wild populations), with wild populations showing evidence of isolation-by-distance among the Nile Delta and upstream riverine populations. Between genetic clusters, approximately 6.9% of SNPs were identified as outliers with outliers identified on all 22 O. niloticus chromosomes. A lack of localized outlier clustering on the genome suggests that no genes of major effect were presently detected. The AS has retained high levels of genetic diversity (Ho_All = 0.21 ± 0.01; He_All = 0.23 ± 0.01) when compared to wild populations (Ho_All = 0.18 ± 0.01; He_All = 0.17 ± 0.01) after 11 years of domestication and selective breeding. Additionally, 565 SNPs were unique within the AS line. While these private SNPs may be due to domestication signals or founder effects, it is suspected that introgression with blue tilapia (Oreochromis aureus) has occurred. This study highlights the importance of understanding the effects of domestication in addition to wild population structure to inform future management and dissemination decisions. Furthermore, by conducting a baseline genetic study of wild populations prior to the dissemination of a domestic line, the effects of aquaculture on these populations can be monitored over time.

Comparison of GWA statistical methods for traits under different genetic structures: A simulation study

Several methods have been used to perform genome wide association (GWA) studies, aiming to map quantitative trait loci (QTL) and candidate variants. The single-step genomic best linear unbiased prediction (ssGBLUP) method is one alternative to perform GWA, which allows the simultaneous use of genotypic, pedigree and phenotypic information. Bayesian multiple regression models have also been used to perform GWA, allowing specifying different priori distribution for the molecular marker effects. The aim of the present study was to evaluate, through simulation, the performance of different methods in the identification of QTLs for polygenic and major gene traits, under different heritabilities when only relatively few animals were genotyped. We also investigated the consequence of considering the agreement among results from different methods as a strategy to decrease errors associated with false positives in QTL mapping. For polygenic scenarios, results showed low power to detect QTL, irrespective of the method, and the use of phenotypes from non-genotyped animals slightly helped QTL detection of ssGBLUP and weighted ssGBLUP (wssGBLUP). For scenarios with major gene effects, there was greater power in QTL detection, with a slight superiority of Bayes C over the other methods. The inclusion of additional phenotypic information (from non-genotyped animals) harmed the performance of wssGBLUP in the presence of major QTL. When only consensus regions identified by different methods were considered as evidence of QTL, the percentage of top windows containing a true QTL tended to increase with the number of methods that identified a top window, for all scenarios. However, an important proportion of true QTL were identified only by a single or few methods. Despite the small differences among methods in the QTL detection, for polygenic traits, the ssGBLUP and wssGBLUP methods seemed to show better results in comparison to the other methods mainly in the low heritability scenario. For traits with major gene effects, the Bayes C method is expected to present better results, compared to the other methods evaluated, given a limited number of genotyped animals. The strategy to use agreement of GWA results among methods to map QTL helps to reduce false positives but comes at a cost of missing important QTL, irrespective of the genetic structure of the trait.

Major-effect candidate genes identified in cultivated strawberry (Fragaria\u2009\xd7\u2009ananassa Duch.) for ellagic acid deoxyhexoside and pelargonidin-3-O-malonylglucoside biosynthesis, key polyphenolic compounds

Strawberries are rich in polyphenols which impart health benefits when metabolized by the gut microbiome, including anti-inflammatory, neuroprotective, and antiproliferative effects. In addition, polyphenolic anthocyanins contribute to the attractive color of strawberry fruits. However, the genetic basis of polyphenol biosynthesis has not been extensively studied in strawberry. In this investigation, ripe fruits from three cultivated strawberry populations were characterized for polyphenol content using HPLC-DAD-MSn and genotyped using the iStraw35k array. GWAS and QTL analyses identified genetic loci controlling polyphenol biosynthesis. QTL were identified on four chromosomes for pelargonidin-3-O-malonylglucoside, pelargonidin-3-O-acetylglucoside, cinnamoyl glucose, and ellagic acid deoxyhexoside biosynthesis. Presence/absence of ellagic acid deoxyhexoside and pelargonidin-3-O-malonylglucoside was found to be under the control of major gene loci on LG1X2 and LG6b, respectively, on the F. × ananassa linkage maps. Interrogation of gene predictions in the F. vesca reference genome sequence identified a single candidate gene for ellagic acid deoxyhexoside biosynthesis, while seven malonyltransferase genes were identified as candidates for pelargonidin-3-O-malonylglucoside biosynthesis. Homologous malonyltransferase genes were identified in the F. × ananassa ‘Camarosa’ genome sequence but the candidate for ellagic acid deoxyhexoside biosynthesis was absent from the ‘Camarosa’ sequence. This study demonstrated that polyphenol biosynthesis in strawberry is, in some cases, under simple genetic control, supporting previous observations of the presence or absence of these compounds in strawberry fruits. It has also shed light on the mechanisms controlling polyphenol biosynthesis and enhanced the knowledge of these biosynthesis pathways in strawberry. The above findings will facilitate breeding for strawberries enriched in compounds with beneficial health effects.