Favorable Haplotypes Research Articles

Transcription factors GmERF1 and GmWRKY6 synergistically regulate low phosphorus tolerance in soybean.

Soybean (Glycine max) is a major grain and oil crop worldwide, but low phosphorus (LP) in soil severely limits the development of soybean production. Dissecting the regulatory mechanism of the phosphorus (P) response is crucial for improving the P use efficiency of soybean. Here, we identified a transcription factor, GmERF1 (ethylene response factor 1), that is mainly expressed in soybean root and localized in the nucleus. Its expression is induced by LP stress and differs substantially in extreme genotypes. The genomic sequences of 559 soybean accessions suggested that the allelic variation of GmERF1 has undergone artificial selection, and its haplotype is significantly related to LP tolerance. GmERF1 knockout or RNA interference resulted in significant increases in root and P uptake efficiency traits, while the overexpression of GmERF1 produced an LP-sensitive phenotype and affected the expression of 6 LP stress-related genes. In addition, GmERF1 directly interacted with GmWRKY6 to inhibit transcription of GmPT5 (phosphate transporter 5), GmPT7, and GmPT8, which affects plant P uptake and use efficiency under LP stress. Taken together, our results show that GmERF1 can affect root development by regulating hormone levels, thus promoting P absorption in soybean, and provide a better understanding of the role of GmERF1 in soybean P signal transduction. The favorable haplotypes from wild soybean will be conducive to the molecular breeding of high P use efficiency in soybean.

Genome-Wide Association Mapping of QTL Underlying Groat Protein Content of a Diverse Panel of Oat Accessions

Groat protein content (GPC) is a key quality trait attribute in oat. Understanding the variation of GPC in oat germplasms and identifying genomic regions associated with GPC are essential for improving this trait. In this study, the GPC of 174 diverse oat accessions was evaluated in three field trials. The results showed a wide variation in GPC, ranging from 6.97% to 22.24% in this panel. Hulless oats displayed a significantly higher GPC compared to hulled oats across all environments. A GWAS analysis was performed based on 38,313 high-quality SNPs, which detected 27 non-redundant QTLs with 41 SNPs significantly associated with GPC. Two QTLs on chromosome 6C (QTL16) and 4D (QTL11) were consistently detected in multiple environments, with QTL16 being the most significant and explaining the highest proportion of the phenotypical variation in all tested environments except in CZ20. Haplotype analysis showed that the favorable haplotypes for GPC are more prevalent in hulless oats. These findings provide a foundation for future efforts to incorporate favorable alleles into new cultivars through introgression, fine mapping, and cloning of promising QTLs.

CandiHap: a haplotype analysis toolkit for natural variation study.

The online version contains supplementary material available at 10.1007/s11032-023-01366-4.

Integrating GWAS and transcriptomics to identify candidate genes conferring heat tolerance in rice.

Rice (Oryza sativa L.) production is being challenged by global warming. Identifying new loci and favorable alleles associated with heat tolerance is crucial to developing rice heat-tolerant varieties. We evaluated the heat tolerance at the seedling stage using 620 diverse rice accessions. A total of six loci associated with heat tolerance were identified by a genome-wide association study (GWAS) with ~2.8 million single nucleotide polymorphisms (SNPs). Among the six detected loci, qHT7 harbored the strongest association signal and the most associated SNPs. By comparing the transcriptomes of two representative accessions with contrasting heat tolerance, LOC_Os07g48710 (OsVQ30) was selected as a promising candidate gene in qHT7 due to the significant difference in its expression level between the two accessions. Haplotype 4 (Hap4) of LOC_Os07g48710 was determined as the favorable haplotype for heat tolerance via the gene-based haplotype analysis. The heat-tolerant haplotype LOC_Os07g48710Hap4 is highly enriched in the tropical Geng/Japonica accessions, and its frequency has decreased significantly during the improvement process of rice varieties. Based on the GWAS and transcriptomics integrated results, a hypothetical model modulated by qHT7 in response to heat stress was proposed. Our results provide valuable candidate genes for improving rice heat tolerance through molecular breeding.

A Haplotype-Based GWAS Identified Trait-Improving QTL Alleles Controlling Agronomic Traits under Contrasting Nitrogen Fertilization Treatments in the MAGIC Wheat Population WM-800.

The multi-parent-advanced-generation-intercross (MAGIC) population WM-800 was developed by intercrossing eight modern winter wheat cultivars to enhance the genetic diversity present in breeding populations. We cultivated WM-800 during two seasons in seven environments under two contrasting nitrogen fertilization treatments. WM-800 lines exhibited highly significant differences between treatments, as well as high heritabilities among the seven agronomic traits studied. The highest-yielding WM-line achieved an average yield increase of 4.40 dt/ha (5.2%) compared to the best founder cultivar Tobak. The subsequent genome-wide-association-study (GWAS), which was based on haplotypes, located QTL for seven agronomic traits including grain yield. In total, 40, 51, and 46 QTL were detected under low, high, and across nitrogen treatments, respectively. For example, the effect of QYLD_3A could be associated with the haplotype allele of cultivar Julius increasing yield by an average of 4.47 dt/ha (5.2%). A novel QTL on chromosome 2B exhibited pleiotropic effects, acting simultaneously on three-grain yield components (ears-per-square-meter, grains-per-ear, and thousand-grain-weight) and plant-height. These effects may be explained by a member of the nitrate-transporter-1 (NRT1)/peptide-family, TaNPF5.34, located 1.05 Mb apart. The WM-800 lines and favorable QTL haplotypes, associated with yield improvements, are currently implemented in wheat breeding programs to develop advanced nitrogen-use efficient wheat cultivars.

Transcriptome and Regional Association Analyses Reveal the Effects of Oleosin Genes on the Accumulation of Oil Content in Brassica napus.

Rapeseed stores lipids in the form of oil bodies. Oil bodies in the seeds of higher plants are surrounded by oleosins. Adjusting oleosin protein levels can prevent the fusion of oil bodies and maintain oil body size during seed development. However, oil contents are affected by many factors, and studies on the complex molecular regulatory mechanisms underlying the variations in seed oil contents of B. napus are limited. In this study, a total of 53 BnOLEO (B. napus oleosin) genes were identified in the genome of B. napus through a genome-wide analysis. The promoter sequences of oleosin genes consisted of various light-, hormone-, and stress-related cis-acting elements, along with transcription factor (TF) binding sites, for 25 TF families in 53 BnOLEO genes. The differentially expressed oleosin genes between two high- and two low-oil-content accessions were explored. BnOLEO3-C09, BnOLEO4-A02, BnOLEO4-A09, BnOLEO2-C04, BnOLEO1-C01, and BnOLEO7-A03 showed higher expressions in the high-oil-content accessions than in low-oil-content accessions, at 25, 35, and 45 days after pollination (DAP) in two different environments. A regional association analysis of 50 re-sequenced rapeseed accessions was used to further analyze these six BnOLEO genes, and it revealed that the nucleotide variations in the BnOLEO1-C01 and BnOLEO7-A03 gene regions were related to the phenotypic variations in seed oil content. Moreover, a co-expression network analysis revealed that the BnOLEO genes were directly linked to lipid/fatty acid metabolism, TF, lipid transport, and carbohydrate genes, thus forming a molecular network involved in seed oil accumulation. These favorable haplotypes can be utilized in molecular marker-assisted selection in order to further improve seed oil contents in rapeseed.

Candidate loci for leaf angle in maize revealed by a combination of genome-wide association study and meta-analysis.

Leaf angle (LA) is a key component of maize plant architecture that can simultaneously govern planting density and improve final yield. However, the genetic mechanisms underlying LA have not been fully addressed. To broaden our understanding of its genetic basis, we scored three LA-related traits on upper, middle, and low leaves of 492 maize inbred lines in five environments. Phenotypic data revealed that the three LA-related traits were normally distributed, and significant variation was observed among environments and genotypes. A genome-wide association study (GWAS) was then performed to dissect the genetic factors that control natural variation in maize LA. In total, 85 significant SNPs (involving 32 non-redundant QTLs) were detected (p ≤ 2.04 × 10-6), and individual QTL explained 4.80%-24.09% of the phenotypic variation. Five co-located QTL were detected in at least two environments, and two QTLs were co-located with multiple LA-related traits. Forty-seven meta-QTLs were identified based on meta-analysis combing 294 LA-related QTLs extracted from 18 previously published studies, 816 genes were identified within these meta-QTLs, and seven co-located QTLs were jointly identified by both GWAS and meta-analysis. ZmULA1 was located in one of the co-located QTLs, qLA7, and its haplotypes, hap1 and hap2, differed significantly in LA-related traits. Interestingly, the temperate materials with hap2 had smallest LA. Finally, we also performed haplotype analysis using the reported genes that regulate LA, and identified a lot of maize germplasms that aggregated favorable haplotypes. These results will be helpful for elucidating the genetic basis of LA and breeding new maize varieties with ideal plant architecture.

Natural variation of Alfin-like family affects seed size and drought tolerance in rice.

The Alfin-like (AL) family is a group of small plant-specific transcriptional factors involved in abiotic stresses in dicotyledon. In an early study, we found an AL gene in rice that was associated with grain yield under drought stress. However, little information is known about the AL family in rice. In this study, AL genes in the rice genome were identified, and the OsAL proteins were found to locate in the nucleus and have no transcriptional self-activation activity. The expression of the OsALs was regulated by different environmental stimulations and plant hormones. Association and domestication analysis revealed that natural variation of most OsALs was significantly associated with yield traits, drought resistance and divergence in grain size in indica and japonica rice varieties. Hap1 of OsAL7.1 and Hap7 of OsAL11 were favorable haplotypes of seed weight and germination under osmotic stress. Furthermore, osal7.1 and osal11 mutants have larger seeds and are more sensitive to abscisic acid and mannitol during germination stage. Overexpressing of OsAL7.1 and OsAL11 in rice weakened the tolerance to drought in the adult stage. Thus, our work provides informative knowledge for exploring and harnessing haplotype diversity of OsALs to improve yield stability under drought stress.

Response of Southeast Asian rice root architecture and anatomy phenotypes to drought stress.

Drought stress in Southeast Asia greatly affects rice production, and the rice root system plays a substantial role in avoiding drought stress. In this study, we examined the phenotypic and genetic correlations among root anatomical, morphological, and agronomic phenotypes over multiple field seasons. A set of >200 rice accessions from Southeast Asia (a subset of the 3000 Rice Genomes Project) was characterized with the aim to identify root morphological and anatomical phenotypes related to productivity under drought stress. Drought stress resulted in slight increases in the basal metaxylem and stele diameter of nodal roots. Although few direct correlations between root phenotypes and grain yield were identified, biomass was consistently positively correlated with crown root number and negatively correlated with stele diameter. The accessions with highest grain yield were characterized by higher crown root numbers and median metaxylem diameter and smaller stele diameter. Genome-wide association study (GWAS) revealed 162 and 210 significant SNPs associated with root phenotypes in the two seasons which resulted in identification of 59 candidate genes related to root development. The gene OsRSL3 was found in a QTL region for median metaxylem diameter. Four SNPs in OsRSL3 were found that caused amino acid changes and significantly associated with the root phenotype. Based on the haplotype analysis for median metaxylem diameter, the rice accessions studied were classified into five allele combinations in order to identify the most favorable haplotypes. The candidate genes and favorable haplotypes provide information useful for the genetic improvement of root phenotypes under drought stress.

Multi‐omics provides new insights into the domestication and improvement of dark jute ( Corchorus olitorius )

Jute (Corchorus sp.) is the most important bast fiber crop worldwide; however, the mechanisms underlying domestication and improvement remain largely unknown. We performed multi-omics analysis by integrating de novo sequencing, resequencing, and transcriptomic and epigenetic sequencing to clarify the domestication and improvement of dark jute Corchorus olitorius. We demonstrated that dark jute underwent early domestication and a relatively moderate genetic bottleneck during improvement breeding. A genome-wide association study of 11 important agronomic traits identified abundant candidate loci. We characterized the selective sweeps in the two breeding stages of jute, prominently, soil salinity differences played an important role in environmental adaptation during domestication, and the strongly selected genes for improvement had an increased frequency of favorable haplotypes. Furthermore, we speculated that an encoding auxin/indole-3-acetic acid protein COS07g_00652 could enhance the flexibility and strength of the stem to improve fiber yield. Our study not only provides valuable genetic resources for future fiber breeding in jute, but also is of great significance for reviewing the genetic basis of early crop breeding.

Genome-wide association study identifies candidate genes and favorable haplotypes for seed yield in Brassica napus.

The online version contains supplementary material available at 10.1007/s11032-022-01332-6.

Effects of Traditional Ethnic Minority Food Culture on Genetic Diversity in Rice Landraces in Guizhou Province, China

Ethnic minorities living in Guizhou Province, China, have produced numerous rice landraces that are rich in genetic variations. Studying the genetic diversity and population structure of rice landraces in Guizhou has therefore become a topic of great research interest. However, the influence of ethnic minorities and their traditional food cultures on rice landraces remains unclear. We analyzed the genetic diversity of 598 rice landraces using simple sequence repeat (SSR) markers. Furthermore, we analyzed the nucleotide variations between two similar populations collected during two different time periods using a single-nucleotide polymorphism (SNP) haplotype analysis of six unlinked nuclear loci. The three major results were as follows: (1) The genetic diversity index of rice landraces in six ecologically distinct rice farming zones of Guizhou Province was high (He = 0.7721), and Southwest Guizhou, which has a large population of ethnic minorities, is the center of genetic diversity of rice landraces in the province; this region had the highest He at 0.7823 and the highest polymorphic information content (PIC) at 0.7562. (2) A neighbor-joining (NJ) phylogenetic tree and a model of the population structure showed that the rice landraces from the southwest, south, and southeast of Guizhou had unique genetic structures and genetic backgrounds, which are closely related to the traditional diet cultures of the local ethnic minorities. (3) A nucleotide variation analysis of similar rice landraces collected in 1980 and 2015 revealed that, after 35 years of domestication by ethnic minorities, the original dominant haplotypes were well-preserved; the frequency of the most favorable haplotypes gradually increased to adapt to the traditional food culture. This study is expected to promote the protection and sustainable utilization of rice landraces from this unique region and to provide valuable germplasm materials and information for future rice breeding and basic research efforts.

Genome-wide association study identifies new loci for 1000-seed weight in Brassica napus

Oilseed rape (Brassica napus L.) is an important oilseed crop worldwide and 1000-seed weight (SW) is the important determinant of seed yield of B. napus. To elucidate the genetic mechanism of SW and mining candidate genes, a panel of 403 diverse B. napus accessions was screened in a genome-wide association study (GWAS) using 1.60 million single-nucleotide polymorphisms (SNPs). This study identified 340 SNPs significantly associated with SW by general linear model (GLM) and mixed linear model (MLM). Through GWAS combined with transcriptome data, two significantly differentially expressed genes were identified as candidate genes (BnaA02g06870D and BnaC06g28920D). Candidate gene association analysis and haplotype analysis showed that the inbred lines carrying ACCC at BnaA02g06870Hap1 and TTGG at BnaC06g28920Hap1 had greater SW than lines carrying other haplotype alleles. Candidate genes and favourable haplotypes identified in this study will be useful for large-seed breeding of B. napus.

A Combination of a Genome-Wide Association Study and a Transcriptome Analysis Reveals circRNAs as New Regulators Involved in the Response to Salt Stress in Maize.

Salinization seriously threatens the normal growth of maize, especially at the seedling stage. Recent studies have demonstrated that circular RNAs (circRNAs) play vital roles in the regulation of plant stress resistance. Here, we performed a genome-wide association study (GWAS) on the survival rate of 300 maize accessions under a salt stress treatment. A total of 5 trait-associated SNPs and 86 candidate genes were obtained by the GWAS. We performed RNA sequencing for 28 transcriptome libraries derived from 2 maize lines with contrasting salt tolerance under normal and salt treatment conditions. A total of 1217 highly expressed circRNAs were identified, of which 371 were responsive to a salt treatment. Using PCR and Sanger sequencing, we verified the reliability of these differentially expressed circRNAs. An integration of the GWAS and RNA-Seq analyses uncovered two differentially expressed hub genes (Zm00001eb013650 and Zm00001eb198930), which were regulated by four circRNAs. Based on these results, we constructed a regulation model of circRNA/miRNA/mRNA that mediated salt stress tolerance in maize. By conducting hub gene-based association analyses, we detected a favorable haplotype in Zm00001eb198930, which was responsible for high salt tolerance. These results help to clarify the regulatory relationship between circRNAs and their target genes as well as to develop salt-tolerant lines for maize breeding.

TaNAC020 homoeologous genes are associated with higher thousand kernel weight and kernel length in Chinese wheat.

NAC proteins constitute one of the largest plant-specific transcription factor (TF) families and play significant roles in plant growth and development. In the present study, three TaNAC020 homoeologous genes located on chromosomes 7A, 7B, and 7D were isolated from wheat (Triticum aestivum L.). TaNAC020s were predominantly expressed in developing grains. The developed transgenic rice lines for TaNAC020-B showed higher starch density and lower amylose contents than those of the wild type (WT). Sequence polymorphism studies showed seven and eight SNPs in TaNAC020-A/B, making three and two haplotypes, respectively. No sequence polymorphism was identified in TaNAC020-D. Association analysis revealed that HAP-2 of TaNAC020-A and TaNAC020-B was the favored haplotype for higher thousand kernel weight and length. Geographic distribution and allelic frequency showed that our favored haplotype experienced strong selection in China, and likewise, diversity increased in TaNAC020s during wheat polyploidization. The results obtained in this study demonstrate that TaNAC020s positively influence starch synthesis and accumulation and are one of the key regulators of the kernel (seed) size and kernel number and have the potential for utilization in wheat breeding to improve grain yield. Molecular markers developed in this study stand instrumental in marker-assisted selection for genetic improvement and germplasm enhancement in wheat.

Biochemical and molecular characterization of sub-tropical maize germplasm for tocopherols

Vitamin E (α-tocopherol) deficiency is one of the serious health concerns among malnutrition in human beings. Exploration of genetic variation for vitamin E in maize germplasm will prove a long-term and cost-effective approach for developing biofortified cultivars. In the present study, 64 maize inbreds were characterized for tocopherols by RP-HPLC and other parameters. A significant genetic variability for α-, γ-, β-, and δ- tocopherols was observed in the germplasm. Maximum δTcontent was present in I188 (7503 ppm) while VL109126 (1499 ppm) showed higher αT content. A positive correlation was observed between αT and carotenoid pigments present in the kernels, whereas αT and oil content showed a negative association. Molecular characterization for αT using VTE4 (ϒ-tocopherol methyltransferase) gene-based InDel marker grouped the germplasm into four distinct haplotypes viz., 0/0 (23), 7/118 (19), 0/118 (14), and 0/7 (8). Three (VL109126, PML224, PML384) and two (MIL41, PML1228) inbreds had 0/0 and 0/118 haplotype, respectively, for the highest αT content. The identified inbreds with favorable αT haplotype could be deployed in maize biofortification programs for the enhancement of vitamin E and also along with other nutritional traits like QPM and β-carotene through marker-assisted backcross breeding to provide nation nutritional security.

The 218th amino acid change of Ser to Ala in TaAGPS-7A increases enzyme activity and grain weight in bread wheat

ADP-glucose pyrophosphorylase (AGPase) influences cereal productivity. There are few reports on the function of cytosolic AGPase small subunit in bread wheat (TaAGPS). In the present study, TaAGPS was preferentially expressed in developing endosperm during grain-filling stages in bread wheat. TaAGPS allelic variations were characterized in 143 wheat accessions by PacBio RS II sequencing. Two haplotypes (TaAGPS-7A-TG and TaAGPS-7A-CT) of TaAGPS-7A were identified and corresponding functional markers were developed, whereas no variants of TaAGPS-7B and TaAGPS-7D were detected. TaAGPS-7A was associated with thousand-kernel weight (TKW) by haplotype–trait association analysis in two populations. Near-isogenic lines (NILs) with TaAGPS-7A-TG showed higher TKW and total kernel starch content than those with TaAGPS-7A-CT, owing to the higher AGPase activity of TaAGPS-7A-TG than TaAGPS-7A-CT both in vitro and in vivo. Overexpression of TaAGPS-7A-TG in bread wheat doubled the transcription levels of TaAGPS and increased AGPase activity by 55.7%, resulting in a 3.0-g higher TKW than in the wild type (WT). Knockdown of TaAGPS led to reduced expression of TaAGPS, AGPase activity, and TKW than in the WT. Thus, owing to the 218th amino acid change of Ser to Ala in TaAGPS-7A, the favorable haplotype TaAGPS-7A-TG showed higher AGPase activity, resulting in higher kernel starch content and grain weight. This finding could be applied to increasing starch content and grain weight in bread wheat.

Allele mining of wheat ABA receptor at TaPYL4 suggests neo-functionalization among the wheat homoeologs

ABA receptors (PYR/PYL/RCAR) play a central role in the water loss control of plants. A previous report indicated that TaPYL4 is a critical gene in wheat that improves grain production under drought conditions and increases water use efficiency. In this study, we analyzed the sequence polymorphisms and genetic effects of TaPYL4s. Based on isolated TaPYL4 genes from chromosomes 2A, 2B and 2D, three haplotypes were detected in the promoter region of TaPYL4-2A, and two haplotypes were present in TaPYL4-2B and TaPYL4-2D, respectively. Marker/trait association analysis indicated that TaPYL4-2A was significantly associated with plant height in 262 Chinese wheat core collection accessions, as well as the drought tolerance coefficient (DTC) for plant height in 239 wheat varieties from Shanxi Province in multiple environments. However, the frequencies of favored drought-tolerant haplotype TaPYL4-2A-Hap2 were considerably low, accounting for only 10%, and lines with this certain Hap could be reserved in the breeding program. TaPYL4-2B was significantly associated with grain number, and the favored haplotype TaPYL4-2B-Hap1 was the dominant allele of above 90% in the collection. For TaPYL4-2D, there were no significant differences in these traits between the two haplotypes in either of the two panels. These results indicate that variation might lead to functional differentiation among the homoeologs and the haplotypes had undergone artificial selection during breeding. Two molecular markers developed to distinguish these haplotypes could be used for breeding in water-limited regions.

The brassinosteroid biosynthesis gene TaD11-2A controls grain size and its elite haplotype improves wheat grain yields.

TaD11-2A affects grain size and root length and its natural variations are associated with significant differences in yield-related traits in wheat. Brassinosteroids (BRs) control many important agronomic traits and therefore the manipulation of BR components could improve crop productivity and performance. However, the potential effects of BR-related genes on yield-related traits and stress tolerance in wheat (Triticum aestivum L.) remain poorly understood. Here, we identified TaD11 genes in wheat (rice D11 orthologs) that encoded enzymes involved in BR biosynthesis. TaD11 genes were highly expressed in roots (Zadoks scale: Z11) and grains (Z75), while expression was significantly suppressed by exogenous BR (24-epiBL). Ectopic expression of TaD11-2A rescued the abnormal panicle structure and plant height (PH) of the clustered primary branch 1 (cpb1) mutant, and also increased endogenous BR levels, resulting in improved grain yields and grain quality in rice. The tad11-2a-1 mutant displayed dwarfism, smaller grains, sensitivity to 24-epiBL, and reduced endogenous BR contents. Natural variations in TaD11-2A were associated with significant differences in yield-related traits, including PH, grain width, 1000-grain weight, and grain yield per plant, and its favorable haplotype, TaD11-2A-HapI was subjected to positive selection during wheat breeding. Additionally, TaD11-2A influenced root length and salt tolerance in rice and wheat at seedling stages. These results indicated the important role of BR TaD11 biosynthetic genes in controlling grain size and root length, and also highlighted their potential in the molecular biological analysis of wheat.

Identification of Haplotypes Associated With Resistance to Bacterial Cold Water Disease in Rainbow Trout Using Whole-Genome Resequencing.

Bacterial cold water disease (BCWD) is an important disease in rainbow trout aquaculture. Previously, we have identified and validated two major QTL (quantitative trait loci) for BCWD resistance, located on chromosomes Omy08 and Omy25, in the odd-year Troutlodge May spawning population. We also demonstrated that marker-assisted selection (MAS) for BCWD resistance using the favorable haplotypes associated with the two major QTL is feasible. However, each favorable haplotype spans a large genomic region of 1.3–1.6 Mb. Recombination events within the haplotype regions will result in new haplotypes associated with BCWD resistance, which will reduce the accuracy of MAS for BCWD resistance over time. The objectives of this study were 1) to identify additional SNPs (single nucleotide polymorphisms) associated with BCWD resistance using whole-genome sequencing (WGS); 2) to validate the SNPs associated with BCWD resistance using family-based association mapping; 3) to refine the haplotypes associated with BCWD resistance; and 4) to evaluate MAS for BCWD resistance using the refined QTL haplotypes. Four consecutive generations of the Troutlodge May spawning population were evaluated for BCWD resistance. Parents and offspring were sequenced as individuals and in pools based on their BCWD phenotypes. Over 12 million SNPs were identified by mapping the sequences from the individuals and pools to the reference genome. SNPs with significantly different allele frequencies between the two BCWD phenotype groups were selected to develop SNP assays for family-based association mapping in three consecutive generations of the Troutlodge May spawning population. Among the 78 SNPs derived from WGS, 77 SNPs were associated with BCWD resistance in at least one of the three consecutive generations. The additional SNPs associated with BCWD resistance allowed us to reduce the physical sizes of haplotypes associated with BCWD resistance to less than 0.5 Mb. We also demonstrated that the refined QTL haplotypes can be used for MAS in the Troutlodge May spawning population. Therefore, the SNPs and haplotypes reported in this study provide additional resources for improvement of BCWD resistance in rainbow trout.