Single Nucleotide Polymorphism Loci Research Articles

利用SNP标记进行水稻品种籼粳鉴定

<p id="C3">Asian cultivated rice (<italic>Oryza sativa</italic> L.) is divided into two subspecies of <italic>xian</italic> and <italic>geng</italic>. With the development of hybrid rice and utilization of interspecific heterosis, the boundaries between <italic>xian</italic> and <italic>geng</italic> are becoming more and more vague. In this study, based on the SNP-index value of 20 million single nucleotide polymorphism (SNP) loci from 3000 rice germplasm resources, we captured 4084 <italic>xian</italic>-<italic>geng</italic> specific SNP loci named as 4k-SNP and used the <italic>xian</italic>-<italic>geng</italic> index as an indicator for <italic>xian</italic>-<italic>geng</italic> identification. Furthermore, the 4k-SNP was reduced to 40-SNP (40 SNP loci) for <italic>indica</italic>/<italic>japonica</italic> identification by using the statistical analysis methods such as large-scale simple random sampling based on the dimensionality reduction algorithms. To verify the effectiveness of 40-SNP on<italic> xian</italic>-<italic>geng</italic> identification, 82 bred varieties were used in this study to compare the results of 40-SNP <italic>xian</italic>-<italic>geng</italic> identification and 4k-SNP identification. The result showed that the <italic>geng</italic> index obtained from 40-SNP and 4k-SNP were very close, and the correlation coefficient was 0.99. Moreover, a total of 49 varieties, belonging to six subgroups (<italic>indica</italic>, <italic>aus</italic>, <italic>rayada</italic>, <italic>aromatic</italic>, <italic>tropical japonica</italic>, and <italic>temperate japonica</italic>), were used to compare the <italic>xian</italic>-<italic>geng</italic> identification results of 40-SNP with those of 4k-SNP and Cheng’s index. And the correlation coefficients of <italic>xian</italic>-<italic>geng</italic> identifications between 40-SNP and 4k-SNP as well as between 40-SNP and Cheng’s index were above 0.98 and 0.86, respectively. These results verified the validity and accuracy of 40-SNP on <italic>xian</italic>-<italic>geng</italic> identification in <italic>Oryza sativa</italic> L. In addition, 40-SNP also had a good distinguishability for the six subgroups in rice, and the <italic>xian</italic>-<italic>geng</italic> index of <italic>indica</italic>, <italic>aus</italic>, <italic>rayada</italic>, <italic>aromatic</italic>, <italic>tropical japonica</italic>, and, <italic>temperate japonica </italic>was less than 0.20, 0.20-0.40, 0.60-0.85, more than 0.90, and 1.00, respectively. This study provides the data and theoretical basis for the differentiation of <italic>xian</italic>-<italic>geng</italic> and the utilization of heterosis and, formulation of seed management regulations.

The relationship between polymorphism of insulin-like growth factor I gene and susceptibility to type 2 diabetes in Uygur population, Xinjiang, China

BackgroundType 2 diabetes (T2DM) susceptibility varies among different populations and is affected by gene single nucleotide polymorphism (SNP). Insulin-like growth factor (IGF)-1 gene, which has many SNP loci, is involved in T2DM pathogenesis. However, the relationship of IGF-1 gene polymorphism with T2DM in Uyghur population is less studied.ObjectiveTo investigate the relationship between T2DM susceptibility and polymorphism of IGF-1 gene in Uyghur population of Xinjiang, China.MethodsThis study enrolled 220 cases (122 males (55.46%) and 98 females (44.54%); mean age of 53.40 ± 10.94 years) of T2DM patients (T2DM group) and 229 (124 males (54.15%) and 105 females (45.85%); mean age of 51.64 ± 10.48 years) healthy controls (control group). Biochemical indexes were determined. IGF-1 gene polymorphism was analyzed by SNP genotyping.ResultsThe levels of TG, HDL, LDL, BUN, and Cr were statistically significant between the T2DM group and the control group. In terms of IGF-1 polymorphism, T2DM group had higher frequency of AA genotype (OR = 2.40, 95% CI = 1.19–4.84) and allele A (OR = 1.55, 95% CI = 1.17–2.06) of rs35767 loci, suggesting that rs35767 is related to the occurrence of T2DM. A total of 5 gene interaction models was obtained through analyzing the interaction of 5 SNP loci with the GMDR method. Among them, the two-factor model that included rs35767 locus and rs5742694 locus had statistical difference with a large cross-validation consistency (10/10). The combination of GG/CC, GA/AA, AA/AA, and AA/AC genotype was in high-risk group, whereas the combination of GG/AA, GG/AC, GA/AC and GA/CC genotype was in the low-risk group. The risk of T2DM in the high-risk group was 2.165 times than that of the low-risk group (OR = 2.165, 95% CI = 1.478–3.171).ConclusionTG, HDL, LDL, BUN, and Cr are influencing factors of T2DM in Uyghur population. The rs35767 locus of IGF-1 gene may be associated with T2DM in Uyghur population. The high-risk group composing of rs35767 locus and rs5742694 locus has a higher risk of T2DM.

Filling gaps in the knowledge of grouper, especially Comb grouper (Mycteroperca acutirostris) (2013-2020) (Copacabana fishery, Rio de Janeiro, Brazil)

There are gaps in our knowledge of important fish consumed by people in tropical countries. Small-scale fisheries are difficult to regulate, especially in countries with no species monitoring. At Copacabana (Rio de Janeiro), we observed 490 individuals of badejo (Comb grouper) (Mycteropeca acutirostris in 2013-2014 and in 2018-2020. The average catch was 1.36 kg (n=466 individuals). A pattern of decreasing catches was observed for Comb grouper. Therefore, provided that the fishing gear and the number of fish have remained the same, the apparent decrease in Comb grouper needs to be further investigated. The results provide information about the major spawning season, around spring (September-December) with additional spawning during April. Genetic analyses in samples from 96 grouper obtained along the coast of Brazil were conducted. The Single Nucleotide Polymorphism (SNP) loci obtained for grouper species enabled us to determine the relative genetic proximity of M. acutirostris and Mycteroperca bonaci, information that can be useful for aquaculture and conservation. The objectives of this study were: a) to obtain data about the fishing activity (catch landings) of Comb groupers at Copacabana, Posto 6; b) to verify the reproductive period of Comb grouper, throughout the year, through the catches from the fishery; c) to develop a large numbers of SNP markers, which can be useful to studies about grouper populations (Mycteroperca and Epinephelus); and, d) to obtain data on the price of the Comb grouper. This study contributes data on the fishery and on the biology and ecology of groupers, and further contributes to conservation efforts.&#x0D; Keywords: comb grouper, fisheries, genetics, Mycteroperca.

Conservation of genetic resources for sustainable aquaculture

Conservation of genetic resources for sustainable aquaculture

Genome-wide association study of the candidate genes for grape berry shape-related traits

BackgroundIn the breeding of new horticultural crops, fruit shape is an important selection characteristic. A variety of fruit shapes appeared during the gradual process of selection and domestication. However, few studies have been conducted on grape berry shape, especially studies related to mining candidate genes. To discover candidate genes related to grape berry shape, the present study first took the berry shape parameters analyzed by Tomato Analyzer as the target traits and used a genome-wide association analysis to analyze candidate genes.ResultsIn total, 122 single-nucleotide polymorphism (SNP) loci had significant correlations with multiple berry shape traits in both years, and some candidate genes were further mined. These genes were mainly related to LRR receptor-like serine/threonine-protein kinase (At1g05700 and At1g07650), transcription factors (GATA transcription factor 23-like, transcription factor VIP1, transcription initiation factor TFIID, and MADS-box transcription factor 6), ubiquitin ligases (F-box protein SKIP19 and RING finger protein 44), and plant hormones (indole-3-acetic acid-amido synthetase GH3.6 and ethylene-responsive transcription factor ERF061). In addition, some important SNP loci were associated with multiple berry-shape traits. The study further revealed some genes that control multiple traits simultaneously, indicating that these berry shape traits are subject to the coordinated regulation of some genes in controlling berry shape.ConclusionsIn the present work, we identified interesting genetic determinants of grape berry shape-related traits. The identification of molecular markers that are closely related to these berry-shape traits is of great significance for breeding specific berry-shaped grape varieties.

Genetic Rescue of the Highly Inbred Norwegian Lundehund.

Augmenting the genetic diversity of small, inbred populations by the introduction of new individuals is often termed “genetic rescue”. An example is the Norwegian Lundehund, a small spitz dog with inbreeding-related health problems that is being crossed with three Nordic breeds, including the Norwegian Buhund. Conservation breeding decisions for the (typically) small number of outcrossed individuals are vital for managing the rescue process, and we genotyped the Lundehund (n = 12), the Buhund (n = 12), their crosses (F1, n = 7) and first-generation backcrosses to the Lundehund (F2, n = 12) with >170,000 single nucleotide polymorphism loci to compare their levels of genetic diversity. We predicted that genome-wide diversity in F2 dogs would be higher than in the Lundehund but lower than in the F1 and the Buhund, and the heterozygosity values showed the expected patterns. We also found that runs of homozygosity, extended chromosomal regions of homozygous genotypes inherited from a common ancestor, were reduced in F2 individuals compared with Lundehund individuals. Our analyses demonstrate the benefits of outcrossing but indicate that some of the acquired genetic diversity is lost following immediate backcrossing. Additional breeding among F2 crosses could therefore merit from further consideration in genetic rescue management.

Genetic Variants and Protein Alterations of Selenium- and T-2 Toxin-Responsive Genes Are Associated With Chondrocytic Damage in Endemic Osteoarthropathy.

The mechanism of environmental factors in Kashin–Beck disease (KBD) remains unknown. We aimed to identify single nucleotide polymorphisms (SNPs) and protein alterations of selenium- and T-2 toxin–responsive genes to provide new evidence of chondrocytic damage in KBD. This study sampled the cubital venous blood of 258 subjects including 129 sex-matched KBD patients and 129 healthy controls for SNP detection. We applied an additive model, a dominant model, and a recessive model to identify significant SNPs. We then used the Comparative Toxicogenomics Database (CTD) to select selenium- and T-2 toxin–responsive genes with the candidate SNP loci. Finally, immunohistochemistry was applied to verify the protein expression of candidate genes in knee cartilage obtained from 15 subjects including 5 KBD, 5 osteoarthritis (OA), and 5 healthy controls. Forty-nine SNPs were genotyped in the current study. The C allele of rs6494629 was less frequent in KBD than in the controls (OR = 0.63, p = 0.011). Based on the CTD database, PPARG, ADAM12, IL6, SMAD3, and TIMP2 were identified to interact with selenium, sodium selenite, and T-2 toxin. KBD was found to be significantly associated with rs12629751 of PPARG (additive model: OR = 0.46, p = 0.012; dominant model: OR = 0.45, p = 0.049; recessive model: OR = 0.18, p = 0.018), rs1871054 of ADAM12 (dominant model: OR = 2.19, p = 0.022), rs1800796 of IL6 (dominant model: OR = 0.30, p = 0.003), rs6494629 of SMAD3 (additive model: OR = 0.65, p = 0.019; dominant model: OR = 0.52, p = 0.012), and rs4789936 of TIMP2 (recessive model: OR = 5.90, p = 0.024). Immunohistochemistry verified significantly upregulated PPARG, ADAM12, SMAD3, and TIMP2 in KBD compared with OA and normal controls (p < 0.05). Genetic polymorphisms of PPARG, ADAM12, SMAD3, and TIMP2 may contribute to the risk of KBD. These genes could promote the pathogenesis of KBD by disturbing ECM homeostasis.

Merging genotyping-by-sequencing data from two ex situ collections provides insights on the pea evolutionary history.

Pea (Pisum sativum L. subsp. sativum) is one of the oldest domesticated species and a widely cultivated legume. In this study, we combined next generation sequencing (NGS) data referring to two genotyping-by-sequencing (GBS) libraries, each one prepared from a different Pisum germplasm collection. The selection of single nucleotide polymorphism (SNP) loci called in both germplasm collections caused some loss of information; however, this did not prevent the obtainment of one of the largest datasets ever used to explore pea biodiversity, consisting of 652 accessions and 22 127 markers. The analysis of population structure reflected genetic variation based on geographic patterns and allowed the definition of a model for the expansion of pea cultivation from the domestication centre to other regions of the world. In genetically distinct populations, the average decay of linkage disequilibrium (LD) ranged from a few bases to hundreds of kilobases, thus indicating different evolutionary histories leading to their diversification. Genome-wide scans resulted in the identification of putative selective sweeps associated with domestication and breeding, including genes known to regulate shoot branching, cotyledon colour and resistance to lodging, and the correct mapping of two Mendelian genes. In addition to providing information of major interest for fundamental and applied research on pea, our work describes the first successful example of integration of different GBS datasets generated from ex situ collections – a process of potential interest for a variety of purposes, including conservation genetics, genome-wide association studies, and breeding.

Coexistence of virulence and β-lactamase genes in avian pathogenic Escherichia coli

Emergence of multidrug resistance in E. coli and advent of newer strains is becoming serious concern which requires keen observations. This study was designed to find the ciprofloxacin resistant E. coli isolates co-existed with multi-drug resistance along with β-lactamase production from poultry source, and finally the genome sequencing of these strains to explore genetic variations. Study constituted on isolation of n = 225 E. coli from broiler farms of central China which were further subjected to identification of resistance against ciprofloxacin followed by antibiogram of n = 26 antibiotics and identification of β-lactamase production. Whole genome resequencing was performed using Illumina HiSeq 4000 system. PCR results revealed predominant β-lactamase genes i.e.CTX-M, CTX-M-1, CTX-M3, TEM-1 and OXA. Furthermore, the MDR isolates were containing most of the tested virulence genes. The most prevalent virulence genes were pap-C, fim-C, fim-H, iuc-D, irp-2, tra-T, iro-N and iut-A. The single nucleotide polymorphisms (SNPs) loci mentioned in this data give valuable genetic markers to growing high-throughput techniques for fine-determination of genotyping of MDR and virulent isolates. Characterization of SNPs on functional basis shed new bits of knowledge on the evolution, disease transmission and pathogenesis of MDR E. coli isolates. In conclusion, these findings provide evidence that most of poultry E. coli are MDR, β-lactamase producers, and virulent which could be a zoonotic threat to the humans. The whole genome resequencing data provide higher resolution of resistance and virulence characteristics in E. coli which can further be used for the development of prevention and treatment strategies.

Genetic Diversity and Population Structure of Sorghum [Sorghum Bicolor (L.) Moench] Accessions as Revealed by Single Nucleotide Polymorphism Markers.

Ethiopia is the center of origin for sorghum [Sorghum bicolor (L.) Moench], where the distinct agro-ecological zones significantly contributed to the genetic diversity of the crops. A large number of sorghum landrace accessions have been conserved ex situ. Molecular characterization of this diverse germplasm can contribute to its efficient conservation and utilization in the breeding programs. This study aimed to investigate the genetic diversity of Ethiopian sorghum using gene-based single nucleotide polymorphism (SNP) markers. In total, 359 individuals representing 24 landrace accessions were genotyped using 3,001 SNP markers. The SNP markers had moderately high polymorphism information content (PIC = 0.24) and gene diversity (H = 0.29), on average. This study revealed 48 SNP loci that were significantly deviated from Hardy–Weinberg equilibrium with excess heterozygosity and 13 loci presumed to be under selection (P < 0.01). The analysis of molecular variance (AMOVA) determined that 35.5% of the total variation occurred within and 64.5% among the accessions. Similarly, significant differentiations were observed among geographic regions and peduncle shape-based groups. In the latter case, accessions with bent peduncles had higher genetic variation than those with erect peduncles. More alleles that are private were found in the eastern region than in the other regions of the country, suggesting a good in situ conservation status in the east. Cluster, principal coordinates (PCoA), and STRUCTURE analyses revealed distinct accession clusters. Hence, crossbreeding genotypes from different clusters and evaluating their progenies for desirable traits is advantageous. The exceptionally high heterozygosity observed in accession SB4 and SB21 from the western geographic region is an intriguing finding of this study, which merits further investigation.

Genome-wide association and linkage mapping strategies reveal genetic loci and candidate genes of phosphorus utilization in soybean

Insufficient available phosphorus in soil has become an important limiting factor for the improvement of yield and quality in soybean. The mining of QTLs and candidate genes controlling soybean phosphorus utilization related traits is a necessary strategy to solve this problem. In this study, 11 phosphorus utilization related traits of a natural population of 281 typical soybean germplasms and a recombinant inbred line (RIL) population of 270 lines were evaluated under different phosphorus conditions at two critical stages: the four-leaf stage as the seedling critical stage was designated as the T1 stage, and the six-leaf stage as the flowering critical stage was designated as the T2 stage. In total, 200 single nucleotide polymorphism (SNP) loci associated with phosphorus utilization related traits were identified in the natural population, including 91 detected at the T1 stage, and 109 detected at the T2 stage. Among these SNP loci, one SNP cluster (s715611375, ss715611377, ss715611379 and ss715611380) on Gm12 was shown to be significantly associated with plant height under the low phosphorus condition at the T1 stage, and the elite haplotype showed significantly greater plant height than the others. Meanwhile, one pleiotropic SNP cluster (ss715606501, ss715606506 and ss715606543) on Gm10 was found to be significantly associated with the ratio of root/shoot, root and total dry weights under the low phosphorus condition at the T2 stage, and the elite haplotype also presented significantly higher values for related characteristics under the phosphorus starvation condition. Furthermore, four co-associated SNP loci (ss715597964, ss715607012, ss715622173 and ss715602331) were identified under the low phosphorus condition at both the T1 and T2 stages, and 12 QTLs were found to be consistent with these genetic loci in the RIL population. More importantly, 14 candidate genes, including MYB transcription factor, purple acid phosphatase, sugar transporter and HSP20-like chaperones superfamily genes, etc., showed differential expression levels after low phosphorus treatment, and three of them were further verified by qRT-PCR. Thus, these genetic loci and candidate genes could be applied in marker-assisted selection or map-based gene cloning for the genetic improvement of soybean phosphorus utilization.

Novel Sources of Resistance to Fusarium oxysporum f. sp. lycopersici Race 3 Among Solanum pennellii Accessions

Fusarium wilt of tomato (Solanum lycopersicum), caused by fungal pathogen Fusarium oxysporum f. sp. lycopersici (Fol), is one of the most important diseases in tomato production. Three races of the pathogen are described, and race-specific resistance genes have been applied in commercial tomato cultivars for controlling the disease. Race 3 (Fol3) threatens tomato production in many regions around the world, and novel resistance resources could expand the diversity and durability of Fol resistance. The wild tomato species, Solanum pennellii, is reported to harbor broad resistance to Fol and was the source of two known Fol3 resistance genes. In this study, we evaluated 42 S. pennellii accessions for resistance to each fusarium wilt race. F1 plants, developed from crossing each accession with the Fol3 susceptible line ‘Suncoast’, were evaluated for Fol3 resistance, and BC1F1 plants were screened to determine the likelihood that Fol3 resistance was based on a novel locus (loci). Nearly all accessions showed resistance to Fol3, and many accessions were resistant to all races. Evaluation of F1 plants indicated a dominant resistance effect to Fol3 from most accessions. Genetic analysis indicated 24 accessions are expected to contain one or more novel Fol3 resistance loci other than an allele near the I-3 locus. To investigate genetic structure of the S. pennellii accessions used in this study, we genotyped all 42 accessions using genotyping by sequencing. Approximately 20% of the single nucleotide polymorphism (SNP) loci were heterozygous across accessions, likely due to the outcrossing nature of the species. Genetic structure analysis at 49,120 unique SNP loci across accessions identified small but obvious genetic differentiations.

Impact of Single Nucleotide Polymorphism in the ANKRD55 Gene on Occurrence and Clinical Characteristics of Rheumatoid Arthritis.

Background:Rheumatoid Arthritis (RA) has multifactorial etiology and numerous genetic and environmental factors have been related to an increased risk of RA. Recently, Genome-Wide Association Studies (GWAS) suggested a large number of Single Nucleotide Polymorphisms (SNPs) loci affecting the susceptibility to RA. One of these loci is rs6859219 (C>A), a functional polymorphism in the ANKRD55 gene which was associated with the expression of ANKRD55 and IL6ST. In the current study, we evaluated the possible association between rs6859219 (intronic variant) in the ANKRD55 gene with RA risk in the Iranian population.Methods:A case-control study using 118 RA patients and 115 healthy counterparts was undertaken in order to determine rs6859219 genotypes using real-time polymerase chain reaction High-Resolution Melting (HRM) method.Results:There was a significant difference in the genotype and allele frequencies of rs6859219 between patients and controls (p<0.001). Logistic regression analysis demonstrates that CC genotype and C allele increased the risk of RA (OR for CC genotype= 7.12; 95%CI [3.51–15.05]/OR for C allele=4.16; 95%CI [2.78–6.28]). Furthermore, regarding the dominant and recessive model of inheritance, RA patients indicated obvious association of the rs6859219 variant compared to healthy controls (p<0.001). Moreover, in the patient group, there was a significant correlation between C-Reactive Protein (CRP) concentration with rs6859219 polymorphism (p<0.001).Conclusion:Our findings propose a substantial correlation between rs6859219 polymorphism and RA risk and clinical characteristics of this disease in the Iranian population.

Transcriptome-wide association study: Opportunity and challenges for cancer studies

Genome-wide association studies (GWAS) have uncovered thousands of single nucleotide polymorphism (SNP) loci that are associated with complex traits. However, the majority of GWAS discoveries are located in non-coding regions and the biological mechanisms behind these associations are not well understood. Transcriptome-wide association studies (TWAS) have gained popularity in recent years by generating biological interpretable discoveries and facilitating the identification of novel associations that have been missed by GWAS. TWAS has identified more than hundreds of susceptibility genes for many complex diseases and traits, including cancers. Here, in this review, we first summarize TWAS methods, then discuss the opportunities for cancer studies and finally review current challenges and future directions for this method.

Strong Association of Polymorphism in SPRED2 Gene with Disease Susceptibility and Clinical Characteristics of Rheumatoid Arthritis in the Iranian Population.

Background:The high heritability of Rheumatoid Arthritis (RA) has been estimated from different studies. Recently, Genome-Wide Association Studies (GWAS) show a large number of Single Nucleotide Polymorphisms (SNPs) loci affecting susceptibility to RA. The rs934734 polymorphism in the SPRED2 gene is one of these loci. Studies have shown that the SPRED2 gene is involved in the regulation of inflammatory response, leukocyte infiltration, and local chemokine production. In the current study, the possible association between SNP rs934734 (intronic variant) in the SPRED2 gene with RA risk in the Iranian population was evaluated.Methods:One hundred fourteen RA patients and 120 healthy counterparts were recruited in this case-control study to evaluate rs934734 genotypes using the real-time PCR High Resolution Melting method (HRM).Results:Logistic regression analysis demonstrated that GG and AG genotypes compared with AA genotype increase the risk of RA (GG vs. AA; OR=4.61; 95%CI [2.21–9.35]; p<0.001 and AG vs. AA; OR=2.54; 95%CI [1.36–4.76]; p=0.004). Furthermore, subjects with allele G were more frequently affected with RA than subjects with A allele (OR=2.33; 95%CI [1.61–3.38]; p<0.001). Besides, in the patient group, there was a significant correlation between Erythrocyte Sedimentation Rate (ESR) and C-reactive protein (CRP) concentration with rs934734 polymorphism (p<0.05).Conclusion:Our findings suggest that rs934734 in SPRED2 strongly underlies RA development and is associated with clinicopathological characteristics of this disease.

Population Structure Analysis and Genome-Wide Association Study of Tea (Camellia sinensis (L.) Kuntze) Germplasm in Qiannan, China, Based on SLAF-Seq Technology

Duyun Maojian tea is a famous tea in China. In this study, the specific-locus amplified fragment (SLAF) sequencing method was used to analyze the population structure and conduct a genome-wide association study (GWAS) of 2 leaf traits of 123 tea plants in Qiannan, China. A total of 462,019 SLAF tags and 11,362,041 single-nucleotide polymorphism (SNP) loci were obtained. The results of phylogenetic tree analysis, cluster analysis, and principal component analysis showed that 123 tea germplasms were clustered into three groups, and the heterozygosity rates for Groups I, II, and II were 0.206, 0.224, and 0.34, respectively. Generally, tea germplasms in a production area are clustered in a group, indicating that tea germplasms in different production areas have certain genetic diversity. The traditional Duyun Maojian tea core production areas, TS and DC-SJ, are clustered into Group I and Group II respectively, while the ZY production area is relatively independent in Group III. Furthermore, based on GWAS analysis, 11 candidate genes related to leaf apex and 7 candidate genes related to leaf shape were obtained. This study clarified the genetic relationship among eight Duyun Maojian tea production areas and obtained candidate genes related to leaf apex and leaf shape development. The results showed that population structure and candidate genes are an effective basis for the breeding of Duyun Maojian tea germplasm.

A Consensus Genetic Map and Linkage Panel for Fresh-market Tomato

The first consensus genetic map in fresh-market tomato (Solanum lycopersicum) was constructed, combining genetic recombination data from two biparental F2 segregating populations derived from four different fresh-market tomatoes. Each F2 population was nominated by different academic tomato breeding programs located in major fresh-market tomato-producing areas of the United States, and chromosome-wide variation in recombination rates was observed between tomato populations based on the origin of their breeding programs. A consensus map constructed using 335 common single nucleotide polymorphism (SNP) sites found in both populations spanned 737.3 cM across 12 tomato chromosomes, with chromosome 2 containing more than 40% of the total SNPs and chromosomes 4, 5, 7, and 10 together representing less than 10% of the SNPs. There was a high degree of collinearity between the genetic and physical positions of those 335 SNP markers. The integration of 6553 SNP sites that were detected in either of the two populations with 335 common sites resulted in an extended consensus genetic map. The total length of the extended map was estimated to be 1997.9 cM, which was compatible with a previous estimate for large-fruited fresh-market tomato. A linkage panel for fresh-market tomato was also established using the combined dataset of the consensus map of 335 SNP loci and 73 SNP-genotyped core fresh-market tomatoes. An empirical genetic mapping study of the tomato brachytic trait using the linkage panel demonstrated the value of the consensus map and linkage panel for tomato research. The allelic information in the linkage panel will serve as a basis for SNP marker implementation, such as genotyping platforms and genomic association map, in tomato.

Statistic Value for Determination of Parents-child Relationship using Single Nucleotide Polymorphisms (SNPs) 44 Loci in Thai Individuals

The current report determined the the parent-child relationship based upon 44 SNPs markers by iPLEX® ProSample ID Panel using statistic values of paternity index (PI). The sample study had two groups: True parent-child(n= 38 families) and unrelated groups (n=38 families). The results showed that the true parent-child group shared44 loci (38 families: 100%), and the unrelated groups had loci mismatch between 2 to 13 loci. The four mismatchloci was the highest number of families (10 families: 26.32%). The maximum and minimum of PI values were1.0120x107 and 83.9371 were among the true parent-child groups. The unrelated group’s maximum and minimumPI values were 5.0065x104 and 7.0750, respectively. The lower limit of the distribution of the true parent-childintersected with the upper limit of the distribution of the unrelated between the values of 83.9371 to 5.0065 × 104. Inthis range of values, the distribution of the PI values could not be used to determine the relationship and thereforewas recognized as a “gray zone”. However, if eliminated mismatch for calculating relatedness of PI, it made thegray zone not allow for clear identification. This research showed that the difference between true parent-childand unrelated groups using 44 SNPs loci typing could help predict human relationships and be applied in otherrelationships in the future.

Assessing the effectiveness of DNA barcoding for exploring hidden genetic diversity in deep-sea fishes

The numbers of deep-sea fish species and their genetic diversities are poorly understood because of taxonomic confusion and the lack of robust diagnostic features. However, DNA barcoding using mitochondrial DNA sequences may offer an effective approach to identifying cryptic species and characterizing their genetic diversities. To validate the genetic differentiation identified by DNA mitochondrial barcoding, it is necessary to show that these reflect variations present in nuclear genomic markers. Here, we performed DNA barcoding using cytochrome c oxidase subunit I (COI) sequences and also carried out multiplexed intersimple sequence repeat genotyping by sequencing (MIG-seq) for mesopelagic and demersal fish species from the continental shelf and upper slope of the northwestern Pacific Ocean. We obtained the COI sequences of 115 species from 48 families; the species were identified using the Barcode of Life Data System. Phylogenetic analyses using COI sequences showed high levels of intraspecific genetic differentiation (Kimura 2-parameter distances &gt;2%) in 20 of 115 species, suggesting many cryptic species or intraspecific genetic differentiation previously unknown in these species. We performed phylogenetic and population genetic analyses using multiple single-nucleotide polymorphism loci obtained by MIG-seq of 3 species that showed high levels of intraspecific genetic differentiation in COI sequences. The nuclear markers confirmed the genetic differentiation in all 3 species identified by the COI sequences. The high concordance between these different genetic markers indicates the effectiveness of DNA barcoding for identifying cryptic deep-sea species and characterizing genetic differentiation in these species.

Genome-wide signatures in flax pinpoint to adaptive evolution along its ecological gradient

Flax is one of the eight founder crops of agriculture. It is believed to have been domesticated as a long-day plant that has since spread to survive in a wide range of eco-geographic regions extending from the warm Indian subcontinent to the low latitude east African highlands and to the cool and high-latitude Eurasia. Understanding the genetic basis underlying its adaptation and selection events throughout its dispersion is essential to develop cultivars adapted to local environmental conditions.Here we detected genetic signatures of local adaptation and selection events of flax based on 385 accessions from all major flax growing regions of the world using genome scan methods and three genomic datasets: (1) a genome-wide dataset of more than 275K single nucleotide polymorphisms (SNPs), (2) a filtered dataset of 23K SNPs with minor allele frequency >10% and, (3) a 34K exon-derived SNP dataset.Principal component (PC) and fixation index (FS⁢T)-based genome scans yielded consistent outlier SNP loci on chromosomes 1, 8, 9 and 12. Additional loci on chromosomes 3, 7, 8, 10, 11, 13 and 14 were detected using both the PC and FS⁢T methods in two of the three datasets. A genome-environment association (GEA) analysis using the 23K dataset and the first PC of cropping season temperature, day-length and latitude identified significant SNPs on chromosomes 3, 7, 9 and 13.Most of the loci detected by the three methods harbored relevant genes for local adaptation, including some that play roles in day-length, light and other biotic and abiotic stresses responses. Such genetic signatures may help to select pre-breeding materials potentially adapted to specific growing niches prior to field performance trials. Given the current low genotyping cost and freely available environmental data, the genome scans along with GEA can readily provide opportunity to sort out materials suitable to various environmental conditions from large set of germplasm in gene banks and/or in situ, thereby assisting the breeding and genetic conservation efforts.