Marker-assisted Selection Programs Research Articles

Genome-wide association study identifies QTL and candidate genes for grain size and weight in a Triticum turgidum collection.

Wheat breeders are constantly looking for genes and alleles that increase grain yield. One key strategy is finding new genetic resources in the wild and domesticated gene pools of related species with genes affecting grain size. This study explored a natural population of Triticum turgidum (L.) phenotyped for grain weight and size-related traits in three field trials and genotyped with single nucleotide polymorphism markers spread across the entire genome. The genome-wide association study analysis identified 39 quantitative trait loci (QTL) for 1000-kernel weight, grain length, grain width, grain area, and grain aspect consistent in at least two and across environments. Interestingly, 23 QTL for grain-related traits were grouped in nine QTL clusters located on chromosomes 1A, 1B, 2B, 3B, 4B, 5A, and 6B, respectively. Moreover, most of these QTL support findings from previous QTL analyses and are further strengthened by the known functions of the genes (such as BG2, GS5, and SRS3) and their similarity to genes in other cereal species. QTL clusters harbored genes that participate in various metabolic processes potentially involved in seed development, phytohormone signaling, sugar transport, mitogen-activated protein kinases signaling, and transcriptional factors (such as MADS-box and WRKY). Identifying loci controlling grain-related traits will provide information on the genetic resources available to breeders to improve grain yield, as well as the opportunity to develop close gene markers to be used in marker-assisted selection programs.

Assessment of genetic biodiversity and association of micronutrients and agronomic traits using microsatellites and staining methods which accelerates high-micronutrients variety selections within different wheat groups

Evaluation of genetic biodiversity for micronutrients is crucial for breeding high-quality crops and addressing the negative impacts of mineral deficiencies. The objectives of this research were to assess genetic variation and the relationship between grain Fe and Zn levels and agronomic traits in a diverse collection of wheat varieties. Additionally, the study aimed to determine the correlation between microsatellite markers (SSR) and micronutrient quantities. A total of 42 genotypes (Iranian commercial cultivars, landraces, and Afghan and Swiss varieties) were evaluated over a two-year period. Fe and Zn levels were measured using two semi quantitative staining assays and atomic absorption spectrophotometry (AAS) facility. Semi-quantitative staining methods and AAS showed high correlations for micronutrient contents. Landraces exhibited higher Fe (63.79 mg/kg) and Zn (44.76 mg/kg) but lower grain yield compared with commercial cultivars. Heritability estimates ranged 53%-79.43%, suggesting that genetic variance played a higher contribution in the phenotypic variation of traits than environmental factors. Notably, Fe content displayed significant correlations with days to maturity. Canonical correlation analysis (CCA) revealed that Zn content was correlated with four agronomic traits. Evaluation of genetic diversity using SSR markers demonstrated high genetic variation among the genotypes tested. The analysis of polymorphism information content (PIC) indicated that SSR primers had an average PIC of 0.75, with the Xgwm192 primer exhibiting higher PIC than others. Several SSR markers revealed association with micronutrient content that can be used in marker-assisted selection (MAS) programs aimed at selection of high micronutrient genotypes. In conclusion, the findings underscored the substantial genetic diversity present in micronutrient levels among global wheat genotypes, the potential of landraces for micronutrients biofortification of wheat cultivars through cross hybridization, the utility of staining methods for screening high/low micronutrient genotypes, and use of microsatellite markers for marker-assisted breeding aiming to micronutrient improvement in breeding programs.

Combining full-length transcriptome sequencing and next generation sequencing to provide insight into the growth superiority of the hybrid grouper (Cromileptes altivelas (♀) × Epinephelus lanceolatus (♂)).

The hybrid grouper (Cromileptes altivelas, ♀ × Epinephelus lanceolatus, ♂) is an economically important aquaculture species that exhibits certain growth advantages compared to its female parent, Cromileptes altivelas. However, the current understanding of the molecular mechanisms underlying the growth of hybrid groupers is lacking. Herein, we performed full-length transcriptome sequencing and next-generation sequencing on the hybrid grouper and its parents to identify growth-related genes and comprehensively analyze the regulatory mechanism of growth heterosis in the hybrid grouper. Approximately 44.70, 40.44, and 45.32 Gb of single-molecule real-time sequencing data were generated in C. altivelas (Cal), E. lanceolatus (Ela), and the hybrid (Hyb), which were combined into 204,322 non-redundant isoforms using the PacBio sequencing platform. Differentially expressed genes (DEGs) were identified between Hyb and Cal (3,494, 2,125, and 1,487 in brain, liver, and muscle tissues, respectively) and Hyb and Ela (3,415, 2,351, and 1,675 in brain, liver, and muscle tissues, respectively). Then, 27 DEGs (13 in the brain and 14 in the muscle) related to growth traits were identified using cluster and correlation network analysis. Quantitative RT-PCR validated 15 DEGs consistent with transcriptome sequencing (RNA-seq) trends. The Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis revealed that these 15 genes were mainly involved in regulating the actin cytoskeleton, suggesting that this pathway plays an essential role in fish growth. In addition, we found that the phosphatase and tensin homologue (PTEN) is a key regulator of growth heterosis in Hyb. These results shed light on the regulatory mechanism of growth in the Hyb, which is important for marker-assisted selection programs to improve the growth quality of groupers.

Molecular Mapping and Transfer of Quantitative Trait Loci (QTL) for Sheath Blight Resistance from Wild Rice Oryza nivara to Cultivated Rice (Oryza sativa L.).

Sheath blight (ShB) is the most serious disease of rice (Oryza sativa L.), caused by the soil-borne fungus Rhizoctonia solani Kühn (R. solani). It poses a significant threat to global rice productivity, resulting in approximately 50% annual yield loss. Managing ShB is particularly challenging due to the broad host range of the pathogen, its necrotrophic nature, the emergence of new races, and the limited availability of highly resistant germplasm. In this study, we conducted QTL mapping using an F2 population derived from a cross between a partially resistant accession (IRGC81941A) of Oryza nivara and the susceptible rice cultivar Punjab rice 121 (PR121). Our analysis identified 29 QTLs for ShB resistance, collectively explaining a phenotypic variance ranging from 4.70 to 48.05%. Notably, a cluster of four QTLs (qRLH1.1, qRLH1.2, qRLH1.5, and qRLH1.8) on chromosome 1 consistently exhibit a resistant response against R. solani. These QTLs span from 0.096 to 420.1 Kb on the rice reference genome and contain several important genes, including Ser/Thr protein kinase, auxin-responsive protein, protease inhibitor/seed storage/LTP family protein, MLO domain-containing protein, disease-responsive protein, thaumatin-like protein, Avr9/Cf9-eliciting protein, and various transcription factors. Additionally, simple sequence repeats (SSR) markers RM212 and RM246 linked to these QTLs effectively distinguish resistant and susceptible rice cultivars, showing great promise for marker-assisted selection programs. Furthermore, our study identified pre-breeding lines in the advanced backcrossed population that exhibited superior agronomic traits and sheath blight resistance compared to the recurrent parent. These promising lines hold significant potential for enhancing the sheath blight resistance in elite cultivars through targeted improvement efforts.

Allele Frequencies of Genetic Variants Associated with Varroa Drone Brood Resistance (DBR) in Apis mellifera Subspecies across the European Continent.

Implementation of marker-assisted selection (MAS) in modern beekeeping would improve sustainability, especially in breeding programs aiming for resilience against the parasitic mite Varroa destructor. Selecting honey bee colonies for natural resistance traits, such as brood-intrinsic suppression of varroa mite reproduction, reduces the use of chemical acaricides while respecting local adaptation. In 2019, eight genomic variants associated with varroa non-reproduction in drone brood were discovered in a single colony from the Amsterdam Water Dune population in the Netherlands. Recently, a new study tested the applicability of these eight genetic variants for the same phenotype on a population-wide scale in Flanders, Belgium. As the properties of some variants varied between the two studies, one hypothesized that the difference in genetic ancestry of the sampled colonies may underly these contribution shifts. In order to frame this, we determined the allele frequencies of the eight genetic variants in more than 360 Apis mellifera colonies across the European continent and found that variant type allele frequencies of these variants are primarily related to the A. mellifera subspecies or phylogenetic honey bee lineage. Our results confirm that population-specific genetic markers should always be evaluated in a new population prior to using them in MAS programs.

Genetic dissection of green pod yield in dolichos bean, an orphan vegetable legume, using new molecular markers.

In the era of genomic-assisted breeding for crop improvement, developing new molecular markers and validating them for use in breeding programs are the prelude. Dolichos bean is one of the most important vegetable legume crops owing to its nutrient-rich green pods used as vegetables. Limitations in genomic resources, including molecular markers, restrict the accelerated improvement of the crop. In the present investigation, a set of 430 new simple sequence repeat markers was developed from sequence information of a reference variety. These markers included di- and tri-nucleotide repeats. The markers were assayed on an association panel, which was evaluated for green pod yield over 5years. A multi-locus model, FarmCPU, was used to assess the marker-trait association analysis. A total of 106 marker-trait associations were identified using an efficient mixed-model approach. Tri-nucleotide repeats were more informative and predominantly associated with trait. Among these markers, 17 were associated with a high level of significance. Markers LP-D-68 and LP-D-14 were identified with a high level of significance in 5-year pooled data and explained 12.70% and 12% of the phenotypic variance, respectively. These markers associated with a high level of confidence have significant scope for use in marker-assisted selection programmes. Other associated markers may be utilized for improving parents through marker-assisted recurrent selection or genomic selection programs.

Investigating growth associated genomic short tandem repeats (STRs) in a resource population generated through molecular breeding of RIR chicken

The long-term selection based on phenotypes causes loss of variation in performance traits and slows down the genetic progress per generation in the population; genomic selection could restore the variability along with faster genetic progress. Genomic short tandem repeats (STRs) in a resource population of RIR chicken were explored investigating randomly selected 114 pedigreed chicks. Alleles separated through 3.4% MetaPhor agarose gel electrophoresis at ten STR loci, and data recorded on growth traits were analyzed. Twenty-six alleles were resolved with frequencies of 0.1140–0.7632 and > 38.60% for the most frequent alleles at ten STR loci. The most frequent genotypes appeared with frequency >21.93% at different loci. Polymorphic information contents ranged from 0.2961 (LEI0079) to 0.6716 (LEI0071). Effective number of alleles ranged from 1.5662 (LEI0079) to 3.5836 (LEI0071). Mean FIS statistics revealed overall 21.78% heterozygosity deficit. Average heterozygosity ranged from 0.3630 (LEI0079) to 0.7241 (LEI0071). Chi-square and G-square test showed the population in Hardy-Weinberg disequilibrium at nine loci. Chick weight was significantly influenced by the factor of sire, and body weight traits by sex and hatch factors of the birds coded with STR-genotypes. ADL0328-BB genotype had the highest chick weight. LEI0068-BC and LEI0071-CC genotypes showed maximum 28-weeks body weight. MCW0010-AA genotype had the potential bearing of the highest body weight records at 16, 32, 36 and 40 weeks of age. MCW0058-CC genotype revealed the same at 24 and 28 weeks of age. The study impacts on marker assisted selection program for genetic improvement of growth traits in poultry.

Integration of genome-wide association studies, metabolomics, and transcriptomics reveals phenolic acid- and flavonoid-associated genes and their regulatory elements under drought stress in rapeseed flowers.

Biochemical and metabolic processes help plants tolerate the adverse effects of drought. In plants accumulating bioactive compounds, understanding the genetic control of the biosynthesis of biochemical pathways helps the discovery of candidate gene (CG)-metabolite relationships. The metabolic profile of flowers in 119 rapeseed (Brassica napus) accessions was assessed over two irrigation treatments, one a well-watered (WW) condition and the other a drought stress (DS) regime. We integrated information gained from 52,157 single-nucleotide polymorphism (SNP) markers, metabolites, and transcriptomes to identify linked SNPs and CGs responsible for the genetic control of flower phenolic compounds and regulatory elements. In a genome-wide association study (GWAS), of the SNPs tested, 29,310 SNPs were qualified to assess the population structure and linkage disequilibrium (LD), of which several SNPs for radical scavenging activity (RSA) and total flavanol content (TFLC) were common between the two irrigation conditions and pleiotropic SNPs were found for chlorogenic and coumaric acids content. The principal component analysis (PCA) and stepwise regression showed that chlorogenic acid and epicatechin in WW and myricetin in DS conditions were the most important components for RSA. The hierarchical cluster analysis (HCA) showed that vanillic acid, myricetin, gallic acid, and catechin were closely associated in both irrigation conditions. Analysis of GWAS showed that 60 CGs were identified, of which 18 were involved in stress-induced pathways, phenylpropanoid pathway, and flavonoid modifications. Of the CGs, PAL1, CHI, UGT89B1, FLS3, CCR1, and CYP75B137 contributed to flavonoid biosynthetic pathways. The results of RNA sequencing (RNA-seq) revealed that the transcript levels of PAL, CHI, and CYP75B137 known as early flavonoid biosynthesis-related genes and FLS3, CCR1, and UGT89B1 related to the later stages were increased during drought conditions. The transcription factors (TFs) NAC035 and ERF119 related to flavonoids and phenolic acids were upregulated under drought conditions. These findings expand our knowledge on the response mechanisms to DS, particularly regarding the regulation of key phenolic biosynthetic genes in rapeseed. Our data also provided specific linked SNPs for marker-assisted selection (MAS) programs and CGs as resources toward realizing metabolomics-associated breeding of rapeseed.

A synonymous single nucleotide polymorphism (g.36417726C > A) in the Lama2 gene influencing fat deposition is associated with post-partum anestrus interval in Murrah buffalo

Postpartum absence of estrus exhibition known as postpartum anestrus interval (PPAI) for more than 90 days after calving is a concerning issue for dairy buffalo farmers' economy. The PPAI duration is influenced by both management practices and animal genetics. Investigating genetic markers associated with PPAI is crucial for incorporating them into marker-assisted selection programs. Towards this goal, our study focused on exploring potential genetic markers from early postpartum adipose tissue gene networks. We successfully identified 24 Single Nucleotide Polymorphisms (SNPs) within 9 candidate genes. In our initial analysis involving 100 buffaloes, we detected a significant association (P = 0.02267) between a specific synonymous SNP within the Lama2 gene (g.36417726C > A) and PPAI. This finding was subsequently validated (P = 0.02937) in a larger cohort of 415 buffaloes, where the SNP explained 1.36 % of the genetic variance. Intriguingly, buffaloes with the CC genotype of this SNP exhibited a PPAI that was 12.71 ± 3.21 days longer compared to buffaloes with AA and CA genotypes. To gain insight into the functional relevance of this SNP, a computational analysis was performed which indicated that the C allele of the SNP (g.36417726C > A) increased the stability of LAMA2 mRNA compared to the A allele. This computational prediction was corroborated by observing a significant increase (P = 0.01798) in Lama2 gene expression (greater than 8-fold) and higher fat percentage (P < 0.05) in adipose tissue of CC genotypes (48.78 ± 1.87 %) compared to AA genotypes (33.59 ± 4.5 %). Furthermore, we noted a significant (P < 0.05) upregulation of C/ebpβ, Pparγ, Fasn, C/ebpα, and Pnpla2 genes, along with the downregulation of Bmp2 and Ptch1 in CC genotypes as opposed to AA genotypes. This observation suggests the involvement of the Pparγ-mediated pathway in both adipogenesis and lipolysis within CC genotypes. In summary, our comprehensive analysis involving association and functional validation underscores the potential of the SNP (g.36417726C > A) within the Lama2 gene as a promising genetic marker against extended PPAI in Murrah buffalo.

Genomics and Physiology of Chlorophyll Fluorescence Parameters in Hordeum vulgare L. under Drought and Salt Stresses.

To map the genomic regions and control chlorophyll fluorescence attributes under normal, salinity-, and drought-stress conditions in barley (Hordeum vulgare L.) at the seedling stage, an experiment was conducted in 2019-2020 using 106 F8 lines resulting from the cross between Badia × Kavir. Initially, the different chlorophyll fluorescence parameters were evaluated. Under drought stress, the highest decrease was related to REo/CSm (59.56%), and the highest increase was related to dV/dto (77.17%). Also, under salinity stress, the highest decrease was related to Fv/Fo (59.56%), and the highest increase was related to DIo/RC (77.17%). Linkage maps were prepared using 152 SSR polymorphic markers, 72 ISSR alleles, 7 IRAP alleles, 29 CAAT alleles, 27 Scot alleles, and 15 iPBS alleles. The obtained map accounted for 999.2 centi-Morgans (cM) of the barley genome length (92% of the whole barley genome). The results indicated the importance of chromosomes 3, 2, and 7 in controlling ABS/CSm, Area, ETo/CSm, Fm, Fv, and ETo/RC under drought stress. qEToRCD-7, as a major QTL, controlled 18.3% of ETo/RC phenotypic variation under drought stress. Under salinity stress, the regions of chromosomes 2 and 7 (102 cM and 126 cM) controlled the parameters ABS/CSo, Fm, Fo, Fv, TRo/SCo, Area, ETo/CSm, and ETo/CSo. The results showed that chlorophyll fluorescence is an important parameter in the study of drought and salinity effects on barley. This is the first report of the investigation of changes in the genetic structure of quantitative genes controlling the fluorescence parameters associated with barley response to drought and salinity stresses in the Iranian barley RILs population. According to the obtained results, it is possible to use HVPLASC1B and EBmac0713 in normal conditions, ISSR21-2 and ISSR30-4 in drought conditions, and Bmac0047, Scot5-B, CAAT6-C, and ISSR30iPBS2076-4 in saline stress conditions to select genotypes with higher photosynthetic capacity in marker-assisted selection programs.

Detection of two SNPs of the LIPE gene in Holstein-Friesian cows with divergent milk production.

The LIPE gene (lipase E, hormone-sensitive type), also known as hormone-sensitive lipase, acts as a primary regulator of lipid metabolism during lactation in cows. We studied a total of two hundred Holstein-Friesian cows and performed sequencing analysis that revealed two synonymous nucleotide changes within the LIPE gene: a transition change, c.276 T > C in exon 2 (g.50631651 T > C; position 351 of GenBank: ON638900) and a transversion change, c.219C > A in exon 6 (g.50635369C > A; position 1070 of GenBank: ON638901). The observed genotypes were TC and CC for the c.276 T > C SNP and CC and CA for the c.219C > A SNP. Notably, the heterozygous TC genotype of the T351C SNP exhibited a significant association with high milk yield. Furthermore, the T351C SNP displayed significant associations with various milk parameters, including temperature, freezing point, density and the percentages of fat, protein, lactose, solids and solids-not-fat, with the homozygous CC genotype showing higher values. The c.219C > A SNP also demonstrated a significant association with milk composition, with heterozygous genotypes (CA) exhibiting higher percentages of fat, protein, and lactose compared to homozygous genotypes (CC). This effect was consistent among both high and low milk producers for fat and lactose percentages, while high milk producers exhibited a higher protein percentage than low milk producers. These findings highlight the importance of considering the detected SNPs in marker-assisted selection and breeding programs for the identification of high milk-producing Holstein-Friesian cows and potentially other breeds. Moreover, this study strongly supports the fundamental role of the LIPE gene in milk production and composition in lactating animals.

Comparative transcriptome and gene co-expression network analysis identifies key candidate genes associated with resistance to summer mortality in the Pacific oyster (Crassostrea gigas)

The global oyster industry is severely hampered by frequent outbreaks of summer massive mortalities. Selective breeding of disease-resistant broodstock is considered as a key strategy to address this problem, and marker-assisted selection programs would help develop oyster lines that are resistance to summer mortality. However, there is currently a need to identify candidate genes associated with disease resistance and to develop molecular markers based on these genes. To identify candidate genes associated with summer mortality resistance, we selected three most resistant and three most susceptible oyster families and compared their basal transcriptomes. A total of 59 families were tested in two sites, and there were significant differences in summer survival among families of different genetic backgrounds. Principal component analysis showed that there was significant clustering of different resistant families, suggesting that the molecular mechanisms underlying the development of resistance characteristics in different resistant families may be similar. Interestingly, transcriptome results showed that the highly expressed genes in resistant families were mainly associated with innate immunity, especially some pattern recognition receptors, including C-type lectins, fibrinogen-related proteins and scavenger receptors. Some transient receptor potential family genes showed differential expression in the both resistant and susceptible families, which may be related to the thermal tolerance of oysters. Notably, some genes related to antioxidant responses and detoxification were highly expressed in resistant families, such as glutathione S-transferase and Cytochrome P450, suggesting that oysters with summer mortality resistance may have greater antioxidant and detoxification capacities. In addition, weighted gene co-expression network analysis (WGCNA) identified three modules that were significantly positively associated with summer survival. The network map of key modules allows us to identify a series of hub genes, such as PEAR1, MCT12, RPL23, TRPM2, MFAP4, TLN1, SCARF1, GAL9 and ACOD. Overall, our study provides new insight into summer mortality resistance by employing comparative transcriptome and WGCNA, and the genes identified in this study should be further investigated for use in marker-assisted selection breeding programs.

Genome-Wide Datasets of Chicories (Cichorium intybus L.) for Marker-Assisted Crop Breeding Applications: A Systematic Review and Meta-Analysis.

Cichorium intybus L. is the most economically important species of its genus and among the most important of the Asteraceae family. In chicory, many linkage maps have been produced, several sets of mapped and unmapped markers have been developed, and dozens of genes linked to traits of agronomic interest have been investigated. This treasure trove of information, properly cataloged and organized, is of pivotal importance for the development of superior commercial products with valuable agronomic potential in terms of yield and quality, including reduced bitter taste and increased inulin production, as well as resistance or tolerance to pathogens and resilience to environmental stresses. For this reason, a systematic review was conducted based on the scientific literature published in chicory during 1980-2023. Based on the results obtained from the meta-analysis, we created two consensus maps capable of supporting marker-assisted breeding (MAB) and marker-assisted selection (MAS) programs. By taking advantage of the recently released genome of C. intybus, we built a 639 molecular marker-based consensus map collecting all the available mapped and unmapped SNP and SSR loci available for this species. In the following section, after summarizing and discussing all the genes investigated in chicory and related to traits of interest such as reproductive barriers, sesquiterpene lactone biosynthesis, inulin metabolism and stress response, we produced a second map encompassing 64 loci that could be useful for MAS purposes. With the advent of omics technologies, molecular data chaos (namely, the situation where the amount of molecular data is so complex and unmanageable that their use becomes challenging) is becoming far from a negligible issue. In this review, we have therefore tried to contribute by standardizing and organizing the molecular data produced thus far in chicory to facilitate the work of breeders.

Application of SVR-Mediated GWAS for Identification of Durable Genetic Regions Associated with Soybean Seed Quality Traits.

Soybean (Glycine max L.) is an important food-grade strategic crop worldwide because of its high seed protein and oil contents. Due to the negative correlation between seed protein and oil percentage, there is a dire need to detect reliable quantitative trait loci (QTL) underlying these traits in order to be used in marker-assisted selection (MAS) programs. Genome-wide association study (GWAS) is one of the most common genetic approaches that is regularly used for detecting QTL associated with quantitative traits. However, the current approaches are mainly focused on estimating the main effects of QTL, and, therefore, a substantial statistical improvement in GWAS is required to detect associated QTL considering their interactions with other QTL as well. This study aimed to compare the support vector regression (SVR) algorithm as a common machine learning method to fixed and random model circulating probability unification (FarmCPU), a common conventional GWAS method in detecting relevant QTL associated with soybean seed quality traits such as protein, oil, and 100-seed weight using 227 soybean genotypes. The results showed a significant negative correlation between soybean seed protein and oil concentrations, with heritability values of 0.69 and 0.67, respectively. In addition, SVR-mediated GWAS was able to identify more relevant QTL underlying the target traits than the FarmCPU method. Our findings demonstrate the potential use of machine learning algorithms in GWAS to detect durable QTL associated with soybean seed quality traits suitable for genomic-based breeding approaches. This study provides new insights into improving the accuracy and efficiency of GWAS and highlights the significance of using advanced computational methods in crop breeding research.

Identification of Growth-Related SNPs and Genes in the Genome of the Pearl Oyster (Pinctada fucata) Using GWAS

Pinctada fucata, the pearl oyster, is a bivalve primarily cultivated for the production of saltwater pearls. In this study, the genome-wide association study (GWAS) for the growth-related traits and a principal components analysis (PCA) in P. fucata were performed. Genomic parameters of 6 growth-related traits in 60 individuals were estimated by using 4,937,162 single-nucleotide polymorphisms (SNPs). A total of 45 SNPs associated with growth traits were thus identified. Furthermore, 165 candidate genes were identified, including collagen alpha-3 (VI), serine/threonine-protein kinase mos-like harboring significant markers, and histidine-rich protein PFHRP-III-like, which may influence growth-related traits associated with various biological processes. The results of this study can facilitate marker-assisted selection and breeding programs designed to enhance growth and also offer a theoretical foundation for the further development and utilization of genomic resources in P. fucata.

Genetic markers associated with divergent selection against the parasite Marteilia cochillia in common cockle (Cerastoderma edule) using transcriptomics and population genomics data

The common cockle (Cerastoderma edule) plays an important role in marine ecosystems and represents a valuable socioeconomic resource for coastal communities. In 2012, the cockle beds from Rı́a de Arousa (Galicia, NW Spain) were seriously decimated by the protozoan Marteilia cochillia responsible for marteiliosis. We aimed to identify single nucleotide polymorphisms (SNP) markers potentially associated with resilience to marteiliosis to be used in marker-assisted selection programs for restoring affected cockle beds and recovering their production. For this, we carried out a population genomics approach using 2b-RADseq, where 38 naive samples (before the first detection of M. cochillia in 2012) from two beds of Rı́a de Arousa were compared with 39 affected samples collected in 2018/2019 (after several years of marteiliosis occurring in the area), collected either before (15 non-exposed samples) or during (24 exposed samples) the marteiliosis outbreak. Additionally, 767 differentially expressed genes (DEG) from a previous transcriptomic study addressed during the aforementioned 2018/19 marteiliosis outbreak, were evaluated to identify SNPs showing signals of selection. Using 2b-RADseq, 9,154 SNPs were genotyped and among them, 110 consistent outliers for divergent selection were identified. This set of SNPs was able to discriminate the samples according to their marteiliosis status (naive vs affected; exposed vs non-exposed), while another 123 SNPs were identified linked to DEGs associated with the level of infection across a temporal series. Finally, combining the population genomics and transcriptomics information, we selected the 60 most reliable SNPs associated with marteiliosis resilience. These SNPs were close to or within DEGs, and many of them were related to immune response (phagocytosis and cell adhesion), defence, such as apoptosis, stress, and cellular cycle, among other functions. This set of SNPs will eventually be validated to develop a cost-effective genotyping tool for their application for obtaining cockle-resilient strains for marteiliosis.

Single nucleotide polymorphisms within exon four of the prolactin gene and their effect on milk traits in cattle populations of Ethiopia

Bovine prolactin (PRL) gene is essential for the initiation and maintenance of lactation and exerts multiple effects on mammary alveoli to promote the synthesis and secretion of major components of milk. The objectives of this study were to identify mutations in PRL gene and to evaluate the mutations as potential markers of milk performance traits in cattle populations of Ethiopia. For this purpose, genomic DNA from whole blood was extracted through salting out procedure from 87 animals of five cattle populations of Ethiopia. Accordingly, three single nucleotide polymorphisms (SNPs) were identified of which one SNP g.8323T > A showed missense mutation while the other two SNPs revealed silent mutations. FST values showed statistically significant genetic differentiation among the studied populations. Intermediate polymorphic information content was noted for most SNPs, which indicates the presence of sufficient genetic variation at this locus. Two SNPs showed heterozygote deficiency as a result of positive FIS values. Only g.8398A > G SNP have statistically significant (p < 0.05) effect on average daily milk yield, fat and solid not fat percentage in all studied cattle populations. Therefore, g.8398A > G SNP identified in this study influences cattle milk production and may be used as possible candidate SNP for marker-assisted selection programs in cattle populations of Ethiopia.

Genome-Wide Association Study of Agronomic and Physiological Traits Related to Drought Tolerance in Potato

Potato (Solanum tuberosum L.) is often considered a water-sensitive crop and its production can be threatened by drought events, making water stress tolerance a trait of increasing interest. In this study, a panel of 144 tetraploid potato genotypes was evaluated for two consecutive years (2019 and 2020) to observe the variation of several physiological traits such as chlorophyll content and fluorescence, stomatal conductance, NDVI, and leaf area and circumference. In addition, agronomic parameters such as yield, tuber fresh weight, tuber number, starch content, dry matter and reducing sugars were determined. GGP V3 Potato array was used to genotype the population, obtaining a total of 18,259 high-quality SNP markers. Marker-trait association was performed using GWASpoly package in R software and Q + K linear mixed models were considered. This approach allowed us to identify eighteen SNP markers significantly associated with the studied traits in both treatments and years, which were related to genes with known functions. Markers related to chlorophyll content and number of tubers under control and stress conditions, and related to stomatal conductance, NDVI, yield and reducing sugar content under water stress, were identified. Although these markers were distributed throughout the genome, the SNPs associated with the traits under control conditions were found mainly on chromosome 11, while under stress conditions they were detected on chromosome 4. These results contribute to the knowledge of the mechanisms of potato tolerance to water stress and are useful for future marker-assisted selection programs.

Introgression of the QTL qSB11-1TT conferring sheath blight resistance in rice (Oryza sativa) into an elite variety, UKMRC 2, and evaluation of its backcross-derived plants.

Sheath blight (SB) is the most damaging fungal disease in rice caused by a soil-borne pathogenic fungus, Rhizoctonia solani Kuhn (R. solani). The disease resistance in rice is a complex quantitative trait controlled by a few major genes. UKMRC2 is a newly developed elite rice variety that possesses high yield potential but is susceptible to sheath blight disease indicating a huge risk of varietal promotion, mass cultivation, and large-scale adoption. The aim of our present study was the development of varietal resistance against R. solani in UKMRC2 to enhance its stability and durability in a wide range of environments and to validate the effects of an SB-resistance QTL on the new genetic background. In our study, we developed 290 BC1F1 backcross progenies from a cross between UKMRC2 and Tetep to introgress the QTL qSBR11-1TT into the UKMRC2 genetic background. Validation of the introgressed QTL region was performed via QTL analysis based on QTL-linked SSR marker genotyping and phenotyping against R. solani artificial field inoculation techniques. The QTL qSBR11-1TT was then authenticated with the results of LOD score (3.25) derived from composite interval mapping, percent phenotypic variance explained (14.6%), and additive effect (1.1) of the QTLs. The QTL region was accurately defined by a pair of flanking markers K39512 and RM7443 with a peak marker RM27360. We found that the presence of combination of alleles, RM224, RM27360 and K39512 demonstrate an improved resistance against the disease rather than any of the single allele. Thus, the presence of the QTL qSBR11-1TT has been validated and confirmed in the URMRC2 genetic background which reveals an opportunity to use the QTL linked with these resistance alleles opens an avenue to resume sheath blight resistance breeding in the future with marker-assisted selection program to boost up resistance in rice varieties.

Genome-wide association study reveals novel candidate genes for litter size in Markhoz goats.

The Markhoz goat is the only breed that can produce high-quality fiber called mohair in Iran; however, the size of its population has faced a dramatic decline during the last decades, mainly due to the reluctance of farmers to rear Markhoz goats caused by a reduction in goat production income. Litter size at birth (LSB) and weaning (LSW) are two economically important reproductive traits for local goat breeders and have the potential of increasing the population growth rate. The present study was aimed to identify possible genomic regions that are associated with LSB and LSW in Markhoz goats using a genome-wide association study (GWAS). To this end, 136 Markhoz goats with record(s) of kidding were selected for GWAS using the Illumina Caprine 50K bead chip. The individual breeding values (BV) of available LSB and LSW records estimated under an animal mixed model were used as the dependent variable in the GWAS, thereby incorporating repeated categorical variables of litter size. Four SNPs on chromosomes 2, 20 and 21 were identified to be significantly associated (FDR p < 0.05) with LSB after multiple testing correction under a Bayesian-information and Linkage-disequilibrium Iteratively Nested Keyway (BLINK) model. Least-square analysis was performed to investigate the effects of detected genotypes on LSB. Ultimately, the GWAS results introduced six candidate genes, including GABRA5, AKAP13, SV2B, PPP1R1C, SSFA2 and TRNAS-GCU in a 100 kb adjacent region of the identified SNPs. Previous studies proposed functional roles of GABRA5 and AKAP13 genes in reproductive processes; however, the role of other candidate genes in reproduction is not clear. These findings warrant further investigation for use in marker-assisted selection programs in Markhoz goats.