Single Nucleotide Polymorphism Markers Research Articles

Genetic Diversity and Population Structure Analysis of Soybean [Glycine max (L.) Merrill] Genotypes Using Agro-Morphological Traits and SNP Markers

Background/Objectives: Understanding the genetic diversity of soybean genotypes can provide valuable information that guides parental selection and the design of an effective hybridization strategy in a soybean breeding program. In order to identify genetically diverse, complementary, and prospective parental lines for breeding, this study set out to ascertain the genetic diversity, relationships, and population structure among 35 soybean genotypes based on agro-morphological traits and Single Nucleotide Polymorphic (SNP) marker data. Methods/Results: Cluster analysis, based on agro-morphological traits, grouped the studied genotypes into four clusters. The first two principal components accounted for 62.8% of the total phenotypic variation, where days to 50% flowering, days to 95% maturity, grain yield, shattering score, and lodging score had high and positive contributions to the total variation. Using the SNP marker information, mean values of 0.16, 0.19, 0.067, and 0.227 were obtained for minor allele frequency (MAF), polymorphic information content (PIC), observed heterozygosity (Ho), and expected heterozygosity (He), respectively. Using different clustering approaches (admixture population structure, principal component scatter plot, and hierarchical clustering), the studied genotypes were grouped into four major clusters. Conclusions:The agro-morphological and molecular analysis results indicated the existence of moderate genetic diversity among the studied genotypes. The traits identified to be significantly related to yield provide valuable information for the genetic improvement of soybeans for yield.

RNA-seq and whole-genome re-sequencing reveal Micropterus salmoides growth-linked gene and selection signatures under carbohydrate-rich diet and varying temperature

This study was performed on Micropterus salmoides to determine growth-linked gene and single nucleotide polymorphism (SNP) markers under carbohydrate diet and varying temperature through RNA-seq and whole-genome re-sequencing. The results showed that growth-related genes were primarily enriched in the fat digestion and absorption signaling pathway, playing a role in lipid transport and metabolism. Fatty acid binding protein 6, bile salt-activated lipase-like, lysophosphatidylcholine acyltransferase 2, phospholipase A2, minor isoenzyme-like, and phospholipase A2, group IB (pancreas) were identified as the crucial genes. The differentially expressed genes between high and low temperatures were enriched in the pentose phosphate pathway, with carbohydrate transport and metabolism were most affected by temperature. Major facilitator superfamily domain containing 10, phosphogluconate dehydrogenase, fructose-1,6-bisphosphatase 1a, and spinster homolog 3 transcript variant X1(spns3) were the shared genes affected by temperature. From all the common genes, 10 growth-associated SNP markers were identified. The TT genotype at rs7781 was associated with lower body weight, while AA genotype at rs31434173 and CC genotype at rs31435313 showed positive correlation with body weight. Analogously, the GG genotype at rs31436887 and AA genotype at rs31438769 also found to characterize better growth performance. At low temperature, individuals with the AA genotype at rs11506587 and rs31435313 exhibited the slowest growth. For the genotypes labeled with rs11510589, the GG individual grew faster than the AA individual, whereas the opposite phenomenon occurred in these genotypes when labeled with rs11511314. The genotypes at rs32970704 and rs32967921 showed no growth correlation. The AA genotype at rs31435313 in spns3 had the slowest growth under a carbohydrate-rich diet regardless of the temperature. Our study presents candidate genes and SNP markers associated with growth influenced by carbohydrate and temperature, providing basis for the development of M. salmoides strain that better accepts carbohydrate diets at varying temperature.

Genetic Diversity and Population Structure of Cacao (Theobroma cacao L.) Germplasm from Sierra Leone and Togo Based on KASP–SNP Genotyping

Cacao (Theobroma cacao L.) is a tropical tree species belonging to the Malvaceae, which originated in the lowland rainforests of the Amazon. It is a major agricultural commodity, which contributes towards the Gross Domestic Product of West African countries, where it accounts for about 70% of the world’s production. Understanding the genetic diversity of genetic resources in a country, especially for an introduced crop such as cacao, is crucial to their management and effective utilization. However, very little is known about the genetic structure of the cacao germplasm from Sierra Leone and Togo based on molecular information. We assembled cacao germplasm accessions (235 from Sierra Leone and 141 from Togo) from different seed gardens and farmers’ fields across the cacao-producing states/regions of these countries for genetic diversity and population structure studies based on single nucleotide polymorphism (SNP) markers using 20 highly informative and reproducible KASP–SNPs markers. Genetic diversity among these accessions was assessed with three complementary clustering methods, including model-based population structure, discriminant analysis of principal components (DAPC), and phylogenetic trees. STRUCTURE and DAPC exhibited some consistency in the allocation of accessions into subpopulations or groups, although some discrepancies in their groupings were noted. Hierarchical clustering analysis grouped all the individuals into two major groups, as well as several sub-clusters. We also conducted a network analysis to elucidate genetic relationships among cacao accessions from Sierra Leone and Togo. Analysis of molecular variance (AMOVA) revealed high genetic diversity (86%) within accessions. A high rate of mislabeling/duplicate genotype names was revealed in both countries, which may be attributed to errors from the sources of introduction, labeling errors, and lost labels. This preliminary study demonstrates the use of KASP–SNPs for fingerprinting that can help identify duplicate/mislabeled accessions and provide strong evidence for improving accuracy and efficiency in cacao germplasm management as well as the distribution of correct materials to farmers.

Identification of Candidate Genes for Soybean Storability via GWAS and WGCNA Approaches

Soybean (Glycine max (L.) Merr.) is an important crop for both food and feed, playing a significant role in agricultural production and the human diet. During long-term storage, soybean seeds often exhibit reduced quality, decreased germination, and lower seedling vigor, ultimately leading to significant yield reductions in soybean crops. Seed storage tolerance is a complex quantitative trait controlled by multiple genes and is also influenced by environmental factors during seed formation, harvest, and storage. This study aimed to evaluate soybean germplasms for their storage tolerance, identify quantitative trait nucleotides (QTNs) associated with seed storage tolerance traits, and screen for candidate genes. The storage tolerance of 168 soybean germplasms was evaluated, and 23,156 high-quality single nucleotide polymorphism (SNP) markers were screened and analyzed through a genome-wide association study (GWAS). Ultimately, 14 QTNs were identified as being associated with seed storage tolerance and were distributed across the eight chromosomes of soybean, with five QTNs (rs25887810, rs27941858, rs33981296, rs44713950, and rs18610980) being newly reported loci in this study. In the linkage disequilibrium regions of these SNPs, 256 genes were identified. By combining GWAS and weighted gene co-expression network analysis (WGCNA), eight hub genes (Glyma.03G058300, Glyma.04G1921100, Glyma.04G192600, Glyma.04G192900, Glyma.07G002000, Glyma.08G329400, Glyma.16G074600, Glyma.16G091400) were jointly identified. Through the analysis of expression patterns, two candidate genes (Glyma.03G058300, Glyma.16G074600) potentially involved in seed storage tolerance were ultimately identified. Additionally, haplotype analysis revealed that natural variations in Glyma.03G058300 could affect seed storage tolerance. The findings of this research provide a theoretical foundation for understanding the regulatory mechanism underlying soybean storage.

Identification of candidate genes associating with soybean cyst nematode in soybean (Glycine max L.) using BSA-seq.

Soybean cyst nematode disease represents the major soil-borne disease of soybean. Identifying disease-resistant genes in soybean has a substantial impact on breeding of disease-resistant crops and genetic improvement. The present work created the F2 population with the disease-resistant line H-10 and disease-susceptible line Chidou4. 30 respective F2disease-resistant and disease-susceptible individuals for forming two DNA pools for whole-genome re-sequencing were selected. As a result, a total of 11,522,230 single nucleotide polymorphism (SNPs) markers from these two parental lines and two mixed pools were obtained. Accordng to SNP-index based association analysis, there were altogether 741 genes out of 99% confidence interval, which were mainly enriched into regions of 38,524,128∼39,849,988 bp with a total length of 1.33 Mb contain 111 genes on chromosome 2, 27,821,012∼29,612,574 bp with a total length of 1.79 Mb contain 92 genes on chromosome 3, 308∼348,214 bp with a total of length 0.35 Mb contain 34 genes on chromosome 10, and 53,867,581∼58,017, 852 bp with a total length of 4.15 Mb contain 504 genes on chromosome 18. Bulk segregant analysis in F2 generations (BSA-seq) was correlated with a disease resistance interval containing 15 genes. Then, using bioinformatics analysis and differential expression analysis, five candidate genes were identified: Glyma.02G211400, Glyma.18G252800, Glyma.18G285800, Glyma.18G287400 and Glyma.18G298200. Our results provides a key basis for analyzing the soybean resistance mechanism against soybean cyst nematode and cloning soybean resistance genes.

Genome-Wide Association Study for Seed Yield of Tepary Bean Using Whole-Genome Resequencing

Tepary bean (Phaseolus acutifolius A. Gray) is a diploid legume species (2n = 2x = 22). It is the most drought- and heat-tolerant crop of the genus Phaseolus. Tepary bean is native to the northern part of Mexico and the south-western part of the U.S. The lack of molecular markers associated with agronomic traits such as 100-seed weight and seed yield limit the development of elite tepary bean cultivars. Therefore, the objectives of this study were to evaluate tepary bean for 100-seed weight and yield, and identify single-nucleotide polymorphism (SNP) markers associated with these traits. A total of 230,000 high-quality SNPs obtained from the whole-genome resequencing of 153 tepary bean accessions were used for this study. For 100-seed weight, a total of 5 and 20 SNPs were found using a mixed linear model (MLM) and compressed mixed linear model (cMLM), respectively. A candidate gene, Phacu.CVR.002G320800.13, encoding the squamosa promoter-binding protein-like (SBP domain) transcription factor family protein was found to be associated with 100-seed weight. For seed yield, a total of one and eight SNPs were identified using an MLM and cMLM, respectively. Phacu.CVR.009G294200.1, encoding for peroxidase family protein, was identified as a candidate gene for seed yield. Both Phacu.CVR.002G320800.13 and Phacu.CVR.009G294200.1 are likely to be involved in seed development of tepary bean. This is one of the few studies investigating the genetics of 100-seed weight and seed yield in tepary bean.

GWAS for Drought Resilience Traits in Red Clover (Trifolium pratense L.)

Red clover (Trifolium pratense L.) is a well-appreciated grassland crop in temperate climates but suffers from increasingly frequent and severe drought periods. Molecular markers for drought resilience (DR) would benefit breeding initiatives for red clover, as would a better understanding of the genes involved in DR. Two previous studies, as follows, have: (1) identified phenotypic DR traits in a diverse set of red clover accessions; and (2) produced genotypic data using a pooled genotyping-by-sequencing (GBS) approach in the same collection. In the present study, we performed genome-wide association studies (GWAS) for DR using the available phenotypic and genotypic data. Single nucleotide polymorphism (SNP) calling was performed using GBS data and the following two red clover genome assemblies: the recent HEN-17 assembly and the Milvus assembly. SNP positions with significant associations were used to delineate flanking regions in both genome assemblies, while functional annotations were retrieved from Medicago truncatula orthologs. GWAS revealed 19 significant SNPs in the HEN-17-derived SNP set, explaining between 5.3 and 23.2% of the phenotypic variation per SNP–trait combination for DR traits. Among the genes in the SNP-flanking regions, we identified candidate genes related to cell wall structuring, genes encoding sugar-modifying proteins, an ureide permease gene, and other genes linked to stress metabolism pathways. GWAS revealed 29 SNPs in the Milvus-derived SNP set that explained substantially more phenotypic variation for DR traits, between 5.3 and 42.3% per SNP–trait combination. Candidate genes included a DEAD-box ATP-dependent RNA helicase gene, a P-loop nucleoside triphosphate hydrolase gene, a Myb/SANT-like DNA-binding domain protein, and an ubiquitin–protein ligase gene. Most accessions in this study are genetically more closely related to the Milvus genotype than to HEN-17, possibly explaining how the Milvus-derived SNP set yielded more robust associations. The Milvus-derived SNP set pinpointed 10 genomic regions that explained more than 25% of the phenotypic variation for DR traits. A possible next step could be the implementation of these SNP markers in practical breeding programs, which would help to improve DR in red clover. Candidate genes could be further characterized in future research to unravel drought stress resilience in red clover in more detail.

Genome-wide association study of salt tolerance at the seed germination stage in lettuce.

Developing lettuce varieties with salt tolerance at the seed germination stage is essential since lettuce seeds are planted half an inch deep in soil where salt levels are often highest in the salinity-affected growing regions. Greater knowledge of genetics and genomics of salt tolerance in lettuce will facilitate breeding of improved lettuce varieties with salt tolerance. Accordingly, we conducted a genome-wide association study (GWAS) in lettuce to identify marker-trait association for salt tolerance at the seed germination stage. The study involved 445 diverse lettuce accessions and 56,820 single nucleotide polymorphism (SNP) markers obtained through genotype-by-sequencing technology using lettuce reference genome version v8. GWAS using two single-locus and three multi-locus models for germination rate (GR) under salinity stress, 5 days post seeding (GR5d_S) and a salinity susceptibility index (SSI) based on GR under salinity stress and control conditions, 5 days post seeding (SSI_GR5d) revealed 10 significant SNPs on lettuce chromosomes 2, 4, and 7. The 10 SNPs were associated with five novel QTLs for salt tolerance in lettuce, explaining phenotyping variations of 5.85%, 4.38%, 4.26%, 3.77%, and 1.80%, indicating the quantitative nature of these two salt tolerance-related traits. Using the basic local alignment search tool (BLAST) within 100 Kb upstream and downstream of each of the 10 SNPs, we identified 25 salt tolerance-related putative candidate genes including four genes encoding for major transcription factors. The 10 significant salt tolerance-related SNPs and the 25 candidate genes identified in the current study will be a valuable resource for molecular marker development and marker-assisted selection for breeding lettuce varieties with improved salt tolerance at the seed germination stage.

Paleoasian Substrate in the Gene Pool of Koryaks According to Data on Autosomal SNP Polymorphism and Y-Chromosome Haplogroups

The gene pool of the Koryaks was studied in comparison with other Far Eastern and Siberian peoples using a genome-wide panel of autosomal single-nucleotide polymorphic markers and Y-chromosome markers. The results of analyzing the frequencies of autosomal SNPs using various methods, the similarity in the composition of Y-chromosome haplogroups and YSTR haplotypes indicate that the gene pool of the Koryaks is as close as possible to the Chukchi one and was formed as a result of the unification of several groups whose ancestors moved from the territory of modern Yakutia and the Amur region. The two dominant Y-chromosome haplogroups of the Koryaks with different sublineages and haplotype clusters demonstrate their contacts with the Chukchi, Evens, Yukaghirs and Eskimos. Analysis of the composition of genetic components and IBD blocks on autosomes indicates the maximum genetic proximity of the Koryaks to the Chukchi. Among the Siberian populations, the Chukchi, Koryaks and Nivkhs form a separate cluster from the main group of Siberian populations, while the Chukchi and Koryaks are more closely related. Far Eastern populations are divided in full accordance with geographic localization into the northern group (Chukchi and Koryaks) and the southern group, including the Nivkhs and Udege. A more detailed analysis of the component composition of gene pools in some populations reveals components specific to them. The isolation of such components is associated with founder effects and a shift in allele frequencies for these populations. The Koryaks and Chukchi are one of the most striking examples of long-standing genetic kinship. In their populations, maximum values of the level of genomic inbreeding FROH 1.5 (0.0422, 0.0409) were found, which is natural due to their relative isolation.

Guadeloupe and Haiti's coffee genetic resources reflect the crop's regional and global history

Societal Impact StatementDespite strong historical declines, Guadeloupe and Haiti's coffee sectors remain important to rural communities' livelihood and resilience. Coffee also holds value as part of the islands' historical legacy and cultural identities. Furthermore, it is often grown in agroforestry systems providing important ecosystem services, which will become more important as these vulnerable islands work to adapt to a changing climate. Current efforts to revitalize coffee farms and target strategically important specialty markets would benefit from understanding existing genetic resources and the historical factors that shaped them. Our study reveals the rich history reflected in current coffee stands on the islands.Summary The West Indies, particularly former French colonies like Haiti and Guadeloupe, were central to the spread of coffee in the Americas. The histories of these Islands are shared until the 19th century, where they diverged significantly. Still, both Islands experienced a strong decline in their coffee sector. Characterizing the genetic and varietal diversity of their coffee resources and understanding historical factors shaping them can help support revitalization efforts. To that end, we performed Kompetitve Allele‐Specific PCR (KASP) genotyping of 80 informative single nucleotide polymorphism (SNP) markers on field samples from across main coffee‐growing region of Guadeloupe, and two historically important ones in Haiti, as well as 146 reference accessions from international collections. We also compared bioclimatic variables from sampled geographic areas and searched for historical determinants of present coffee resources. At least five Coffea arabica varietal groups were found in Haiti, versus two in Guadeloupe, with admixed individuals in both. The traditional Typica variety is still present in both islands, growing across a variety of climatic environments. We also found Coffea canephora on both islands, with multiple likely origins, and identified C. liberica var. liberica in Guadeloupe. These differences are explained by the Islands' respective histories. Overall, Guadeloupe experienced fewer, but older introductions of non‐Typica coffee. By contrast, several recent introductions have taken place in Haiti, driven by local and global factors and reflecting the history of Arabica varietal development and spread. Diversity on these islands is dynamic, and our results reveal opportunities and limits to the future of Guadeloupean and Haitian coffee.

Traces of Paleolithic expansion in the Nivkh gene pool based on data on autosomal SNP and Y chromosome polymorphism.

The Nivkhs are a small ethnic group indigenous of the Russian Far East, living in the Khabarovsk Territory and on Sakhalin Island, descending from the ancient inhabitants of these territories. In the Nivkhs, a specific Sakhalin-Amur anthropological type is prevalent. They are quite isolated, due to long isolation from contacts with other peoples. The gene pool of the Nivkhs and other Far Eastern and Siberian populations was characterized using a genome-wide panel of autosomal single-nucleotide polymorphic markers and Y chromosome haplogroups. Bioinformatic processing of frequencies of autosomal SNPs, Y chromosome haplogroups and YSTR haplotypes showed that the Nivkh gene pool is very different from the other populations'. Analysis of the SNP frequencies using the PCA method divided the Far Eastern populations in full accordance with the territories of their residence into the northern group of the Chukchi and Koryaks and the southern group, including the Nivkhs and Udege. The remoteness of the Nivkhs coincides with their geographic localization, with the Nivkhs and Udege demonstrating the greatest kinship. The Nivkhs have a specific component of their gene pool, which is present with much less frequency in the Udege and Transbaikal Evenks. According to the IBD blocks, the genotypes of the Nivkhs show a very small percentage of coincidence with the Udege, Koryaks, Evenks and Chukchi, the value of which is the lowest compared to the IBD blocks among all other Siberian populations. The Nivkh-specific composition of haplogroups and YSTR haplotypes was shown. In the Nivkhs, the C2a1 haplogroup is divided into three sublines, which have a fairly ancient origin and are associated with the ancestors of modern northern Mongoloids. The Nivkh haplogroup O2a1b1a2a-F238 is found among residents of China and Myanmar. The Q1a1a1-M120 line is represented among the Nivkhs, Koryaks, Evenks and Yukaghirs. Phylogenetic analysis of individual Y chromosomal haplogroups demonstrated the closeness of the Nivkh gene pool with the ancient population of the Amur and Okhotsk regions, the Koryaks, the Tungus peoples and the population of Southeast Asia. The Nivkh gene pool confirms the relative smallness of their ancestral groups without mixing with other populations.

Genome-wide association analysis revealed genetic markers linked to grain yield and yield related traits in finger millet grown in acidic soils

Abstract Aim Soil acidity has a major impact on the finger millet yield and productivity as tolerant cultivars that perform well in acidic soils are limited. This study aimed at evaluating major finger millet phenotypic traits under acidic soils followed by identifying associated markers. Method A total of 288 finger millet genotypes were field evaluated for 8 major phenotypic traits including grain yield under acid soil conditions at two independent locations (Bako and Gute) in Ethiopia. In parallel, the same genotypes were subjected to genotyping-by-sequencing to generate single nucleotide polymorphism markers to be used in the association panel. Results Phenotypic data analysis revealed significant phenotypic variation in all the targeted traits among the studied genotypes. Genotypes Ec-100093, Ec-215803, and Ec-203322 were relatively high-yielding, whereas genotypes Ec-229721 and Ec-242110 had the lowest grain yield across the two locations. The broad-sense heritability of the traits ranged from 0.04 for the number of effective tillers (NET) to 0.78 for days to emergence (DE). The marker-trait association analysis revealed 23 SNP markers significantly associated with one or more traits. Among the 23 significant markers, one marker associated with DE, seven with days to heading (DH), four with days to maturity (DM), one with plant height (PH), two with number of fingers, two with ear length (EL), three with the number of effective tillers (NET) and three with grain yield (GY). Conclusions The identified novel markers associated with the targeted traits will potentially be useful for genomics-driven finger millet improvement in acidic soils.

Genetic diversity, population structure, and a genome-wide association study of sorghum lines assembled for breeding in Uganda.

Sorghum is an important source of food and feed worldwide. Developing sorghum core germplasm collections improves our understanding of the evolution and exploitation of genetic diversity in breeding programs. Despite its significance, the characterization of the genetic diversity of local germplasm pools and the identification of genomic loci underlying the variation of critical agronomic traits in sorghum remains limited in most African countries, including Uganda. In this study, we evaluated a collection of 543 sorghum accessions actively used in Ugandan breeding program across two cropping seasons at NaSARRI, Uganda, under natural field conditions. Phenotypic data analysis revealed significant (p<0.01) variation among accessions for days to 50% flowering, plant height, panicle exsertion, and grain yield, with broad-sense heritability (H²) estimates of 0.54, 0.9, 0.81, and 0.48, respectively, indicating a high genetic variability for these traits. We used a newly developed genomic resource of 7,156 single nucleotide polymorphism (SNP) markers to characterize the genetic diversity and population structure of this collection. On average, the SNP markers exhibited moderately high polymorphic information content (PIC = 0.3) and gene diversity (He = 0.3), while observed heterozygosity (Ho = 0.07) was low, typical for self-pollinating crops like sorghum. Admixture-based models, PCA, and cluster analysis all grouped the accessions into two subpopulations with relatively low genetic differentiation. Genome-wide association study (GWAS) identified candidate genes linked to key agronomic traits using a breeding diversity panel from Uganda. GWAS analysis using three different mixed models identified 12 genomic regions associated with days to flowering, plant height, panicle exsertion, grain yield, and glume coverage. Five core candidate genes were co-localized with these significant SNPs. The SNP markers and candidate genes discovered provide valuable insights into the genetic regulation of key agronomic traits and, upon validation, hold promise for genomics-driven breeding strategies in Uganda.

The Jan Sjödin faba bean mutant collection: morphological and molecular characterization.

Plant mutagenesis creates novel alleles, thereby increasing genetic and phenotypic diversity. The availability of the faba bean (Vicia faba L.) reference genome and a growing set of additional genomic resources has increased the scientific and practical value of mutant collections. We aimed to genotype and morphologically phenotype a historical faba bean mutant collection developed and characterized by Jan Sjödin (1934-2023) over half a century ago in order to increase its value to researchers. The collection was genotyped using high-throughput single-primer enrichment technology (SPET) assays. We used 11,073 informative single nucleotide polymorphism (SNP) markers spanning the faba bean genome to genotype 52 mutant lines along with the background line, cv. Primus. A range of flower, seed, leaf, and stipule mutations were observed. The analysis of population structure revealed a shallow structure with no major subpopulations. Principal component and cluster analyses revealed, to a minor extent, that the mutants clustered by their phenotype. The mutants' phenotypic variation and shallow structure indicate that the Sjödin faba bean collection has the potential to play a significant role in faba bean breeding and in genetic and functional studies.

Analysis of genetic diversity and genetic structure of indigenous chicken populations in Guizhou province based on genome-wide single nucleotide polymorphism markers

Guizhou province in China is rich in indigenous chicken breeds, playing an essential role in the genetic improvement of modern chickens. Genetic diversity has decreased in recent decades due to accelerated breeding processes and changing conservation priorities. To determine the genetic diversity and population structure of Guizhou indigenous chicken breeds, we used 55K genotyping arrays to conduct population genetic analysis on 233 individuals from 8 Guizhou indigenous breeds and 263 individuals from 9 Guizhou indigenous chicken populations. We evaluated the genetic diversity parameter (heterozygosity, proportion of polymorphic markers, and nucleotide diversity), linkage disequilibrium (LD), population structure, and genetic differentiation (FST and genetics distance). Genetic diversity results indicated that the genetic diversity of chicken breeds in Guizhou province is relatively affluent. Among Guizhou breeds, Baiyi black-bone and Guizhou yellow chicken displayed the lowest genetic diversity, as the 2 breeds exhibit lower PN and heterozygosity, the extent of linkage disequilibrium is higher. According to the LD pattern, Guizhou indigenous breeds can be divided into 3 categories. Population structure analysis showed a certain degree of genetic differentiation among local chickens in Guizhou. We argue that Chishui black-bone and Puan black-bone chickens are 2 different geographical regional groups of the same breed. In principal component analysis, individuals from the 2 groups clustered together, and the phylogenetic tree results showed that the 2 groups clustered together to form a branch independent of other breeds, and they displayed an identical pattern of ancestral lineage composition. The research results will provide a reference for protecting local chicken genetic resources in Guizhou Province and promote the protection and utilization of genetic resources.

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

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

Genome-wide association mapping and genomic prediction of water deficit stress tolerance indices in spring bread wheat

Genome-wide association mapping (GWAM) is crucial for identifying the genetic architecture of quantitative traits, such as drought tolerance indices in bread wheat. This study aims to identify Marker-Trait Associations (MTAs) and genes related to drought tolerance indices in wheat. Seven drought tolerance indices were calculated based on grain weight per spike under field drought stress (FDS) and field non-stress (FNS) conditions. These indices included mean productivity (MP), geometric mean productivity (GMP), relative drought index (RDI), stress tolerance index (STI), tolerance index (TOL), stress susceptibility index (SSI), and yield stability index (YSI). Genotyping of the samples was performed using single nucleotide polymorphism (SNP) markers. A total of 96 MTAs were identified for the studied indices and conditions FNS and FDS in this experiment, with a threshold of -log10p ≥ 3.0. These included FNS, FDS, GMP, MP, STI, SSI, RDI, and YSI, with 15, 11, 16, 16, 20, 6, 6, and 6 MTAs, respectively. The MTAs identified for the drought tolerance indices GMP, MP, and STI were located on chromosomes 2 A, 3B, and 6 A, respectively. Moreover, this study identified four genes related to the indices, namely “TraesCS2B02G000100,” “TraesCS3A02G000100,” “TraesCS2B02G000200,” and “TraesCS4B02G000100”. These genes play a crucial role in drought tolerance and can be utilized for marker-assisted selection to enhance drought tolerance wheat genotypes.

Genomic selection for agronomical phenotypes using genome-wide SNPs and SVs in pearl millet.

Pearl millet is an essential crop worldwide, with noteworthy resilience to abiotic stress, yet the advancement of its breeding remains constrained by the underutilization of molecular-assisted breeding techniques. In this study, we collected 1,455,924 single nucleotide polymorphism (SNP) and 124,532 structural variant (SV) markers primarily from a pearl millet inbred germplasm association panel consisting of 242 accessions including 120 observed phenotypes, mostly related to the yield. Our findings revealed that the SV markers had the capacity to capture genetic diversity not discerned by SNP markers. Furthermore, no correlation in heritability was observed between SNP and SV markers associated with the same phenotype. The assessment of the nine genomic prediction models revealed that SV markers performed better than SNP markers. When using the SV markers as the predictor variable, the genomic BLUP model achieved the best performance, while using the SNP markers, Bayesian methods outperformed the others. The integration of these models enabled the identification of eight candidate accessions with high genomic estimated breeding values (GEBV) across nine phenotypes using SNP markers. Four candidate accessions were identified with high GEBV across 22 phenotypes using SV markers. Notably, accession 'P23' emerged as a consistent candidate predicted based on both SNP and SV markers specifically for panicle number. These findings contribute valuable insights into the potential of utilizing both SNP and SV markers for genomic prediction in pearl millet breeding. Moreover, the identification of promising candidate accessions, such as 'P23', underscores the accelerated prospects of molecular breeding initiatives for enhancing pearl millet varieties.

Genomic insights of leafminer resistance in spinach through GWAS approach and genomic prediction

The Leafminers, representing a diverse group of insects from various genera within the Agromyzidae family, pose a significant threat to spinach (Spinacia oleracea L.) production. This study aimed to identify single nucleotide polymorphism (SNP) markers associated with leafminer resistance through a genome-wide association study (GWAS) and to evaluate the prediction accuracy (PA) for selecting resistant spinach using genomic prediction (GP). Using a dataset of 84 301 SNPs obtained from whole-genome resequencing, seven GWAS models, including BLINK, FarmCPU, MLM, and MLMM in GAPIT 3, as well as MLM, GLM, and SMR in TASSEL 5, were employed to perform GWAS on a panel of 286 USDA spinach germplasm accessions. Three SNP markers, namely 1_115279256_C_T, 3_157082529_C_T, and 4_168510908_T_G on chromosomes 1, 3, and 4, respectively, were identified as associated with leafminer resistance. In the 30 kb flanking regions of these markers, four candidate genes (SOV1g031330, SOV1g031340, SOV4g047270, and SOV4g047280), encoding LOB domain-containing protein, KH domain-containing protein, were discovered. Nodulin-like domain-containing protein, and SAM domain-containing protein, were discovered. The PA for leafminer resistance selection was estimated using ten different SNP sets, including two GWAS-derived marker sets (three and 51 SNPs) and eight random marker sets (ranging from 51 to 10 K SNPs) analyzed by seven GP models. The findings emphasized the superior performance of GWAS-derived SNP sets, reaching a PA of up to 0.79 using the cBLUP model. Notably, this research marks the pioneering application of GP in the context of insect resistance, providing a significant advancement in the understanding and management of leafminer resistance in spinach cultivation.

Development and Validation of an SNP Marker for Identifying Xanthomonas oryzae pv. oryzae Thai Isolates That Break xa5-Mediated Bacterial Blight Resistance in Rice.

Xanthomonas oryzae pv. oryzae (Xoo) is a pathogenic bacterium responsible for bacterial blight (BB) disease in rice, primarily mediated by the interaction between the plant and pathogen. The virulence mechanism involves the activation of the Sugars Will Eventually be Exported Transporter (SWEET) gene family in rice by transcription activator-like effectors derived from Xoo. The BB resistance gene xa5 has been identified as one of the most effective genes against Thai Xoo isolates, but xa5-mediated resistance-breaking Xoo strains have emerged. This study aimed to develop a single nucleotide polymorphism (SNP) marker for precise identification of xa5-mediated resistance-breaking Xoo. Comparative genomics of Thai Xoo isolates Xoo16PK001 and Xoo16PK002, which were incompatible and compatible with rice variety IRBB5 carrying xa5, respectively, identified eight SNP positions for the development of an SNP marker. The SNP marker XooE6 yields a specific 1,143 bp PCR product unique to Xoo16PK002. Screening 61 Thai isolates using XooE6 identified two positives: Xoo20PL010 and Xoo20UT002. Inoculation tests on rice varieties IRBB5 and IRBB13 demonstrated compatibility with IRBB5 and incompatibility with IRBB13, which bears Xa5 and xa13. Xoo16PK001 (XooE6-negative) showed different virulence. Inoculation on IRBB21 harboring Xa5, Xa13, and Xa21 resulted in partial resistance to both XooE6-positive and -negative strains. XooE6-positive strains up-regulated SWEET11 and suppressed SWEET14 in IRBB5, while Xoo16PK001 slightly induced SWEET11 but activated SWEET14 in IRBB13. This highlights the potential of XooE6 to identify xa5-mediated resistance-breaking Xoo strains and elucidate their pathogenic mechanisms through the upregulation of SWEET11.