High-density SNPs Research Articles

Enhancing testing efficacy of high-density SNP microarrays to distinguish pedigrees belonging to the same kinship class

Kinship testing, which involves genotyping genetic markers and comparing their profiles between individuals, holds significant applications in forensic science. However, the prevalent use of independent markers often lacks the discriminatory power to distinguish pedigrees belong to the same kinship class. While numerous studies have attempted to address this challenge through diverse approaches, the testing efficacy of high-density SNP microarrays in combination with the likelihood approach remains unclear.In this study, we further explored the utilization of linked autosomal SNPs derived from microarrays with the likelihood approach. Several SNP panels with differing numbers of loci were developed and putative pedigrees were constructed to evaluated to test their efficacy in distinguishing second-degree relationships, including grandparent-grandchild, half-siblings, and avuncular. Our findings indicate that the use of high-density SNP microarrays is theoretically feasible for discriminating second-degree relationships, with balanced classification rates ranging from 0.444 to 0.853.Moreover, to optimize the practical effectiveness of discriminating pedigrees belonging to the same kinship class, several other aspects such as adding additional SNPs or an additional relative and examining the effects of genotype errors and population selection were discussed. Our results revealed that the employment of denser marker sets with more accurate genotyping methods may be beneficial. Additionally, the inclusion of additional relatives and the selection of an appropriate reference population also appear to be crucial factors for enhancing the accuracy of kinship testing.In conclusion, our study provides insights into the potential of high-density SNPs in kinship testing and highlights the need for further optimization and examination into various factors that may contribute to enhancing testing efficacy.

Sea surface temperature and current-related parameters affecting local adaptation of scalloped spiny lobster population in Indonesia’s archipelagic system

The Scalloped Spiny lobster (Panulirus homarus, Linnaeus 1758) known as one of the commercially harvested Panilurid lobster. This species was distributed widely across continents. Indonesia, as one of the largest archipelagic systems in the world, was also distribution area of the Scalloped Spiny lobster. These facts have led to questions regarding spiny lobster harvest and culture management by considering population differentiation and habitat fragmentation on complex and distinct archipelagic islands. Our investigation was conducted using high-density SNPs datasets from several spiny lobsters harvested from five locations in Indonesia. We found strong differentiation among spiny lobster populations clustered into 3 sub-populations. Environment association analysis and Fst analysis revealed outlier loci significantly associated with Sea Surface Temperature variation and potentially correlated with Sea Current-related parameters. The evidence of a structured population of scalloped spiny lobsters in Indonesia can serve as a consideration in the management of spiny lobsters.

PEGylated nanoparticles interact with macrophages independently of immune response factors and trigger a non-phagocytic, low-inflammatory response

Poly-ethylene-glycol (PEG)-based nanoparticles (NPs) - including cylindrical micelles (CNPs), spherical micelles (SNPs), and PEGylated liposomes (PLs) - are hypothesized to be cleared in vivo by opsonization followed by liver macrophage phagocytosis. This hypothesis has been used to explain the rapid and significant localization of NPs to the liver after administration into the mammalian vasculature. Here, we show that the opsonization-phagocytosis nexus is not the major factor driving PEG-NP – macrophage interactions. First, mouse and human blood proteins had insignificant affinity for PEG-NPs. Second, PEG-NPs bound macrophages in the absence of serum proteins. Third, lipoproteins blocked PEG-NP binding to macrophages. Because of these findings, we tested the postulate that PEG-NPs bind (apo)lipoprotein receptors. Indeed, PEG-NPs triggered an in vitro macrophage transcription program that was similar to that triggered by lipoproteins and different from that triggered by lipopolysaccharide (LPS) and group A Streptococcus. Unlike LPS and pathogens, PLs did not increase transcripts involved in phagocytosis or inflammation. High-density lipoprotein (HDL) and SNPs triggered remarkably similar mouse bone-marrow-derived macrophage transcription programs. Unlike opsonized pathogens, CNPs, SNPs, and PLs lowered macrophage autophagosome levels and either reduced or did not increase the secretion of key macrophage pro-inflammatory cytokines and chemokines. Thus, the sequential opsonization and phagocytosis process is likely a minor aspect of PEG-NP – macrophage interactions. Instead, PEG-NP interactions with (apo)lipoprotein and scavenger receptors appear to be a strong driving force for PEG-NP – macrophage binding, entry, and downstream effects. We hypothesize that the high presence of these receptors on liver macrophages and on liver sinusoidal endothelial cells is the reason PEG-NPs localize rapidly and strongly to the liver.

Targeted sequencing of high-density SNPs provides an enhanced tool for forensic applications and genetic landscape exploration in Chinese Korean ethnic group

BackgroundIn this study, we present a NGS-based panel designed for sequencing 1993 SNP loci for forensic DNA investigation. This panel addresses unique challenges encountered in forensic practice and allows for a comprehensive population genetic study of the Chinese Korean ethnic group. To achieve this, we combine our results with datasets from the 1000 Genomes Project and the Human Genome Diversity Panel.ResultsWe demonstrate that this panel is a reliable tool for individual identification and parentage testing, even when dealing with degraded DNA samples featuring exceedingly low SNP detection rates. The performance of this panel for complex kinship determinations, such as half-sibling and grandparent-grandchild scenarios, is also validated by various kinship simulations. Population genetic studies indicate that this panel can uncover population substructures on both global and regional scales. Notably, the Han population can be distinguished from the ethnic minorities in the northern and southern regions of East Asia, suggesting its potential for regional ancestry inference. Furthermore, we highlight that the Chinese Korean ethnic group, along with various Han populations from different regional areas and certain northern ethnic minorities (Daur, Tujia, Japanese, Mongolian, Xibo), exhibit a higher degree of genetic affinities when examined from a genomic perspective.ConclusionThis study provides convincing evidence that the NGS-based panel can serve as a reliable tool for various forensic applications. Moreover, it has helped to enhance our knowledge about the genetic landscape of the Chinese Korean ethnic group.

Accurate genomic selection using low-density SNP panels preselected by maximum likelihood estimation

Genomic selection (GS) poses a challenge for the prediction of the genomic estimated breeding value (GEBV) using a low-density SNP panel. Several methods have been proposed for SNP preselection. However, these methods often suffer from either significant computational complexity or erratic accuracy in GS. In this study, we developed an approach called MLE-rank based on maximum likelihood estimation to preselect a set of SNPs for GS. First, we generated 90 simulated datasets and compared the performance of MLE-rank with uniform distribution and preselection based on a genome-wide association study (GWAS). For simulated datasets, compared to uniform distribution, both MLE-rank and GWAS preselection reduced the SNP density by a factor of 10 while maintaining prediction accuracy. Additionally, compared to the other two methods, MLE-rank's prediction accuracy was significantly improved with the medium- and high-heritability datasets. Then, we further evaluated these three preselection approaches using real disease-resistant phenotypes of leopard coral grouper (Plectropomus leopardus) and Japanese flounder (Paralichthys olivaceus). We found that the 3 k SNPs preselected by MLE-rank had a stable and effective prediction effect. The uniform distribution requires 70 k, while the GWAS preselection method requires 3 k (P. leopardus) and 50 k (P. olivaceus) to achieve similar prediction accuracy. Finally, we evaluated the prediction accuracy of MLE-rank using candidate populations of flounders and their progeny survival rates, with uniform distribution and GWAS preselection as benchmarks. In the results for this dataset, MLE-rank was found to have the same predictive effect for low-density SNP panels as it did for high-density SNPs, regardless of whether GWAS preselection or uniform distribution was used. Taken together, the results we have observed indicate that we have ensured that MLE-rank does not reduce prediction accuracy for any of the datasets. MLE-rank showed superior performance in reducing the number of SNPs. Moreover, we observed a relative standard deviation in prediction accuracy when using a low density of SNPs selected by MLE-rank compared to a high density determined through a uniform distribution strategy. In conclusion, MLE-rank not only reduces the number of SNPs used for GS but also exhibits high predictive accuracy. This could potentially lead to a decrease in genotyping costs and promote the wider application of GS in fish breeding.

Genomic Landscape of Copy Number Variations and Their Associations with Climatic Variables in the World's Sheep.

Sheep show characteristics of phenotypic diversity and adaptation to diverse climatic regions. Previous studies indicated associations between copy number variations (CNVs) and climate-driven adaptive evolution in humans and other domestic animals. Here, we constructed a genomic landscape of CNVs (n = 39,145) in 47 old autochthonous populations genotyped at a set of high-density (600 K) SNPs to detect environment-driven signatures of CNVs using a multivariate regression model. We found 136 deletions and 52 duplications that were significantly (Padj. < 0.05) associated with climatic variables. These climate-mediated selective CNVs are involved in functional candidate genes for heat stress and cold climate adaptation (e.g., B3GNTL1, UBE2L3, and TRAF2), coat and wool-related traits (e.g., TMEM9, STRA6, RASGRP2, and PLA2G3), repairing damaged DNA (e.g., HTT), GTPase activity (e.g., COPG), fast metabolism (e.g., LMF2 and LPIN3), fertility and reproduction (e.g., SLC19A1 and CCDC155), growth-related traits (e.g., ADRM1 and IGFALS), and immune response (e.g., BEGAIN and RNF121) in sheep. In particular, we identified significant (Padj. < 0.05) associations between probes in deleted/duplicated CNVs and solar radiation. Enrichment analysis of the gene sets among all the CNVs revealed significant (Padj. < 0.05) enriched gene ontology terms and pathways related to functions such as nucleotide, protein complex, and GTPase activity. Additionally, we observed overlapping between the CNVs and 140 known sheep QTLs. Our findings imply that CNVs can serve as genomic markers for the selection of sheep adapted to specific climatic conditions.

Challenges in selecting admixture models and marker sets to infer genetic ancestry in a Brazilian admixed population

The inference of genetic ancestry plays an increasingly prominent role in clinical, population, and forensic genetics studies. Several genotyping strategies and analytical methodologies have been developed over the last few decades to assign individuals to specific biogeographic regions. However, despite these efforts, ancestry inference in populations with a recent history of admixture, such as those in Brazil, remains a challenge. In admixed populations, proportion and components of genetic ancestry vary on different levels: (i) between populations; (ii) between individuals of the same population, and (iii) throughout the individual's genome. The present study evaluated 1171 admixed Brazilian samples to compare the genetic ancestry inferred by tri-/tetra-hybrid admixture models and evaluated different marker sets from those with small numbers of ancestry informative markers panels (AIMs), to high-density SNPs (HDSNP) and whole-genome-sequence (WGS) data. Analyses revealed greater variation in the correlation coefficient of ancestry components within and between admixed populations, especially for minority ancestral components. We also observed positive correlation between the number of markers in the AIMs panel and HDSNP/WGS. Furthermore, the greater the number of markers, the more accurate the tri-/tetra-hybrid admixture models.

Whole Genome Sequencing and Morphological Trait-Based Evaluation of UPOV Option 2 for DUS Testing in Rice.

To evaluate the application potential of high-density SNPs in rice distinctness, uniformity, and stability (DUS) testing, we screened 37,929 SNP loci distributed on 12 rice chromosomes based on whole-genome resequencing of 122 rice accessions. These SNP loci were used to analyze the DUS testing of rice varieties based on the correlation between the molecular and phenotypic distances of varieties according to UPOV option 2. The results showed that statistical algorithms and the number of phenotypic traits and SNP loci all affected the correlation between the molecular and phenotypic distances of rice varieties. Relative to the other nine algorithms, the Jaccard similarity algorithm had the highest correlation of 0.6587. Both the number of SNPs and the number of phenotypes had a ceiling effect on the correlation between the molecular and phenotypic distances of varieties, and the ceiling effect of the number of SNP loci was more obvious. To overcome the correlation bottleneck, we used the genome-wide prediction method to predict 30 phenotypic traits and found that the prediction accuracy of some traits, such as the basal sheath anthocyanin color, glume length, and intensity of the green color of the leaf blade, was very low. In combination with group comparison analysis, we found that the key to overcoming the ceiling effect of correlation was to improve the resolution of traits with low predictive values. In addition, we also performed distinctness testing on rice varieties by using the molecular distance and phenotypic distance, and we found that there were large differences between the two methods, indicating that UPOV option 2 alone cannot replace the traditional phenotypic DUS testing. However, genotype and phenotype analysis together can increase the efficiency of DUS testing.

Identification of cold tolerance QTLs at the bud burst stage in 211 rice landraces by GWAS

BackgroundRice is a crop that is very sensitive to low temperature, and its morphological development and production are greatly affected by low temperature. Therefore, understanding the genetic basis of cold tolerance in rice is of great significance for mining favorable genes and cultivating excellent rice varieties. However, there have been limited studies focusing on cold tolerance at the bud burst stage; therefore, considerable attention should be given to the genetic basis of cold tolerance at this stage.ResultsIn this study, a natural population consisting of 211 rice landraces collected from 15 provinces in China and other countries was used for the first time to evaluate cold tolerance at the bud burst stage. Population structure analysis showed that this population was divided into two groups and was rich in genetic diversity. Our evaluation results confirmed that japonica rice was more tolerant to cold at the bud burst stage than indica rice. A genome-wide association study (GWAS) was performed with the phenotypic data of 211 rice landraces and a 36,727 SNP dataset under a mixed linear model. Twelve QTLs (P < 0.0001) were identified for the seedling survival rate (SR) after treatment at 4 °C, in which there were five QTLs (qSR2–2, qSR3–1, qSR3–2, qSR3–3 and qSR9) that were colocalized with those from previous studies and seven QTLs (qSR2–1, qSR3–4, qSR3–5, qSR3–6, qSR3–7, qSR4 and qSR7) that were reported for the first time. Among these QTLs, qSR9, harboring the most significant SNP, explained the most phenotypic variation. Through bioinformatics analysis, five genes (LOC_Os09g12440, LOC_Os09g12470, LOC_Os09g12520, LOC_Os09g12580 and LOC_Os09g12720) were identified as candidates for qSR9.ConclusionThis natural population consisting of 211 rice landraces combined with high-density SNPs will serve as a better choice for identifying rice QTLs/genes in the future, and the detected QTLs associated with cold tolerance at the bud burst stage in rice will be conducive to further mining favorable genes and breeding rice varieties under cold stress.

Mapping of QTL for agronomic traits using high-density SNPs with an RIL population in maize.

Genome wide association studies (GWAS) have been widely used to identify QTLs underlying quantitative traits in humans and animals, and they have also become a popular method of mapping QTLs in many crops, including maize. Advances in high-throughput genotyping technologies enable construction of high-density linkage maps using SNP markers. High-density genetic mapping must precede to find molecular markers associated with a particular trait. The objectives of this study were to (1) construct a high-density linkage map using SNP markers and (2) detect the QTLs for grain yield and quality related traits of the Mo17/KW7 RIL population. In this study, two parental lines, Mo17 (normal maize inbred line) and KW7 (waxy inbred line) and 80 F7:8 lines in the Mo17/KW7 RIL population were genotyped using the MaizeSNP50 BeadChip, an Illumina BeadChip array of 56,110 maize SNPs. Marker integration and detection of QTLs was performed using the inclusive composite interval mapping (ICIM) method within the QTL IciMapping software. This study was genotyped using the Illumina MaizeSNP50 BeadChip for maize Mo17/KW7 recombinant inbred line (RIL) population. The 2904 SNP markers were distributed along all 10 maize chromosomes. The total length of the linkage map was 3553.7cm, with an average interval of 1.22cm between SNPs. A total of 18 QTLs controlling eight traits were detected in the Mo17/KW7 RIL population. Three QTLs for plant height (PH) were detected on chromosomes 4 and 8 and showed from 16.01% (qPH8) to 19.85% (qPH4a) of phenotypic variance. Five QTLs related to ear height (EH) were identified on chromosomes 3, 4, and 6 and accounted for 3.79% (qEH6) to 27.57% (qEH4b) of phenotypic variance. Five QTLs related to water content (WC) on chromosomes 1, 4, 8, and 9 accounted for 9.55% (qWC8b) to 23.30% (qWC4) of phenotypic variance. One QTL (qAC9) relating to amylose content (AC) on chromosome 9 showed 82.10% of phenotypic variance. The high-density linkage map and putative QTLs of the maize RIL population detected in this study can be effectively utilized in waxy and normal maize breeding programs to facilitate the selection process through marker-assisted selection (MAS) breeding programs.

Genomic breed composition of Ningxiang pig via different SNP panels.

The genomic breed composition (GBC) reflects the genetic relationship between individual animal and ancestor breeds in composite or hybrid breeds. Also, it can estimate the genomic contribution of each breed (ancestor) to the genome of each individual animal. Using genomic SNP information to estimate Ningxiang pig GBC is of great significance. First of all, GBC was widely used in cattle and had significant effects, but there is almost no using experience in Chinese endemic pig breeds. Importantly, High-density SNPs are expensive but can be economized by deploying a relatively small number of highly informative SNP scattered evenly across the genome. Moreover, the impact of low-density SNPs selection strategy on estimating the GBC of individual animals has not been fully explained. Using SNP data from different databases and organizations, we established reference (N=2015) and verification (N=302) data sets. Twelve successively smaller SNP panels (500, 1K, 5K, 10K) were built from those SNP in the reference data by three selection methods (uniform, maximized the Euclidean distance (MED) and random distribution method). For each panel, the GBC of Ningxiang pigs in the reference dataset was estimated. Then combining Shannon entropy and the GBC results, the optimal panel (the 10K SNP panel constructed by MED method) was picked out to estimate the GBC of verification Ningxiang pig, which detected that 230 individuals were purebred Ningxiang pigs and the remaining 72 impure individuals contained 6.44% blood related with Rongchang pigs and 4.09% with Bamaxiang pigs in the verification Ningxiang population. Finally, the genetic structure analysis of verification population was performed combining with the results of GBC, multi-dimensional scaling (MDS) analysis and hierarchical cluster analysis. These results showed: (a) GBC could accurately identify purebred Ningxiang pigs and, scientifically, calculate the genomic contribution of each breed of each hybrid animal. (b) GBC could carry out population genetic structure and understand the genetic background of Ningxiang pigs. Such findings highlight a variety of opportunities to better protect and identify other endangered local breeds in China facing the same situation as Ningxiang pig and provide more accurate, economical and efficient new technical support in GBC estimation breeding work.

A conserved haplotype in Wagyu cattle contains RAB4A whose encoded protein regulates glucose trafficking in muscle and fat cells

The Wagyu breed of taurine cattle possess favourable genetics for intramuscular fat (IMF) but genomic loci associated with the trait remain under characterised. Here, we report the identification of a previously unidentified genomic region possessing a particular haplotype structure in Wagyu. Through deployment of a genome-wide haplotype detection analysis that captures regions conserved in a target population but not other populations we screened 100 individual Wagyu and contrasted them with 100 individuals from two independent comparison breeds, Charolais and Angus, using high-density SNPs. An extreme level of Wagyu conservation was assigned to a single genomic window (spanning genomic coordinates BTA28:41088-300265bp). In fact, a five-SNP region spanning 27096bp is almost perfectly conserved among the 100 Wagyu individuals assayed and partially overlaps RAB4A. Focussing in, two consecutive SNPs (genomic coordinates 236949 and 239950) are apparently fixed within the Wagyu (BB and AA respectively), but at mixed frequencies in the other two breeds. These SNPs are located in the two introns straddling exon 7. In a separate analysis using the 1000 Bulls database, we found that, coincident with exon 7 of RAB4A first allele frequencies were highest in the high IMF Japanese Native (Wagyu) breeds (0.78) and lowest in the low IMF indicine breeds (Nelore and Brahman), with intermediate marbling breeds (Angus and Charolais) assigned intermediate rankings (0.42). RAB4A is known to encode a protein that regulates intracellular trafficking of the insulin-regulated glucose transporter GLUT4. RAB4A can be considered an attractive new positional candidate for IMF development.

Deploying viscosity and starch polymer properties to predict cooking and eating quality models: A novel breeding tool to predict texture

Acceptance of new rice genotypes demanded by rice value chain depends on premium value of varieties that match consumer demands of regional preferences. High throughput prediction tools are not available to breeders to classify cooking and eating quality (CEQ) ideotypes and to capture texture of varieties. The pasting properties in combination with starch properties were used to develop two layered models in order to classify the rice varieties into twelve distinct CEQ ideotypes with unique sensory profiles. Classification models developed using random forest method depicted the overall accuracy of 96 %. These CEQ models were found to be robust to predict ideotypes in both Indica and Japonica diversity panels grown under dry and wet seasons and across the years. We conducted random forest modeling using 1.8 million high density SNPs and identified top 1000 SNP features which explained CEQ model classification with the accuracy of 0.81. Furthermore these CEQ models were found to be valuable to predict textural preferences of IRRI breeding lines released during 1960–2013 and mega varieties preferred in South and South East Asia.

Genome-wide association studies in tropical maize germplasm reveal novel and known genomic regions for resistance to Northern corn leaf blight

Northern Corn Leaf Blight (NCLB) caused by Setosphaeria turcica, is one of the most important diseases of maize world-wide, and one of the major reasons behind yield losses in maize crop in Asia. In the present investigation, a high-resolution genome wide association study (GWAS) was conducted for NCLB resistance in three association mapping panels, predominantly consisting of tropical lines adapted to different agro-ecologies. These panels were phenotyped for disease severity across three locations with high disease prevalence in India. High density SNPs from Genotyping-by-sequencing were used in GWAS, after controlling for population structure and kinship matrices, based on single locus mixed linear model (MLM). Twenty-two SNPs were identified, that revealed a significant association with NCLB in the three mapping panels. Haplotype regression analysis revealed association of 17 significant haplotypes at FDR ≤ 0.05, with two common haplotypes across three maize panels. Several of the significantly associated SNPs/haplotypes were found to be co-located in chromosomal bins previously reported for major genes like Ht2, Ht3 and Htn1 and QTL for NCLB resistance and multiple foliar disease resistance. Phenotypic variance explained by these significant SNPs/haplotypes ranged from low to moderate, suggesting a breeding strategy of combining multiple resistance alleles towards resistance for NCLB.

Identification of hybridization and introgression between Cinnamomum kanehirae Hayata and C. camphora (L.) Presl using genotyping-by-sequencing

Cinnamomum kanehirae Hayata and C. camphora (L.) Presl are important tree species in eastern Asia. The wood of C. kanehirae is in increasing demand for culturing Antrodia cinnamomea, a medicinal fungus that naturally grows inside the trunk of C. kanehirae. Putative hybrids between C. kanehirae and C. camphora were previously reported but with no scientific evidence, leading to confusion or misplanting. First, to identify the female parent of putative hybrids, the maternal inheritance InDel (insertion/deletion) markers were developed by using low-coverage sequencing. SNPs were developed by using genotyping-by-sequencing (GBS) approach in C. kanehirae, C. camphora and putative hybrids. The results indicated that the female parent of the studied hybrids was C. camphora. Eight hundred and forty of the 529,006 high-density SNPs were selected and used for analysis. Hybrids were classified as F1 (C. kanehirae × C. camphora), F2 and backcrosses. Hybridization has occurred in the human-developed area of eastern and southwestern Taiwan, and the introgression was bidirectional. For producing pure wood, buffering zones should be established around seed orchards to avoid cross-species pollination and to preserve the genetic purity of C. kanehirae. The DNA markers developed in this study will also be valuable for further wood identification, breeding and evolutionary research.

Heterosis-associated genes confer high yield in super hybrid rice

Key messageHeterosis QTLs, including qSS7 and qHD8, with dominance effects were identified through GBS and large-scale phenotyping of CSSLs and hybrid F1 populations in a paddy field.Heterosis has contributed immensely to agricultural production, but its genetic basis is unclear. We evaluated dominance effects by creating two hybrid populations: a B-homo set with a homozygous background and heterozygous chromosomal segments and a B-heter set with a heterozygous background and homozygous segments. This was achieved by crossing a set of 156 backcrossed-derived chromosome segment substitution lines (CSSLs) with their recurrent parent (9311), the male parent of the first super-high-yield hybrid Liangyoupei9 (LYP9), and with the female parent (PA64s) of the hybrid. The CSSLs were subjected to a genotyping-by-sequencing analysis to develop a genetic map of segments introduced from the PA64s. We evaluated the heterotic effects on eight yield-related traits in the hybrid variety and F1 populations in large-scale field experiments over 2 years. Using a linkage map consisting of high-density SNPs, we identified heterosis-associated genes in LYP9. Five candidate genes contributed to the high yield of LYP9, with qSS7 and qHD8 repeatedly detected in both B-hybrid populations. The heterozygous segments harboring qSS7 and qHD8 showed dominance effects that contributed to the heterosis of yield components in the hybrid rice variety Liangyoupei9.

Genetic Analysis for Cooking and Eating Quality of Super Rice and Fine Mapping of a Novel Locus qGC10 for Gel Consistency.

Rice (Oryza sativa L.) is an important cereal that provides food for more than half of the world’s population. Besides grain yield, improving grain quality is also essential to rice breeders. Amylose content (AC), gelatinization temperature (GT) and gel consistency (GC) are considered to be three indicators for cooking and eating quality in rice. Using a genetic map of RILs derived from the super rice Liang-You-Pei-Jiu with high-density SNPs, we detected 3 QTLs for AC, 3 QTLs for GT, and 8 QTLs for GC on chromosomes 3, 4, 5, 6, 10, and 12. Wx locus, an important determinator for AC and GC, resided in one QTL cluster for AC and GC, qAC6 and qGC6 here. And a novel major QTL qGC10 on chromosome 10 was identified in both Lingshui and Hangzhou. With the BC4F2 population derived from a CSSL harboring the segment for qGC10 from 93-11 in PA64s background, it was fine mapped between two molecular markers within 181 kb region with 27 annotated genes. Quantitative real-time PCR results showed that eight genes were differentially expressed in endosperm of two parents. After DNA sequencing, only LOC_Os10g04900, which encodes a F-box domain containing protein, has 2 bp deletion in the exon of PA64s, resulting in a premature stop codon. Therefore, LOC_Os10g04900 is considered to be the most likely candidate gene for qGC10 associated with gel consistency. Identification of qGC10 provides a new genetic resource for improvement of rice quality.

Identification of genes for salt tolerance and yield-related traits in rice plants grown hydroponically and under saline field conditions by genome-wide association study

BackgroundSoil salinity is one of the main environmental conditions that affects rice production. Identifying the genetic loci that affect rice salt tolerance (ST)-related traits at the seedling stage, especially under saline field conditions, is crucial for ST rice breeding by pyramiding ST genes that act at different developmental stages.ResultsLarge phenotypic variations were observed in 708 rice accessions, and yield and its related traits were considerably limited when exposed to salt stress. In a genome-wide association study (GWAS), 2255 marker-trait association signals were detected for all measured traits, and the significant SNPs were distributed in 903 genes. Of these, 43 genes processed same functional annotation, and the gene ontology terms “biological processes” and “molecular function” with the known genes responsive to salt stress in rice. Further haplotype analysis detected 15 promising candidates significantly associated with the target traits, including five known genes and 10 novel genes. We identified seven accessions carrying favorable haplotypes of four genes significantly associated with grain yield that performed well under saline stress conditions.ConclusionsUsing high density SNPs within genes to conduct GWAS is an effective way to identify candidate genes for salt tolerance in rice. Five known genes (OsMYB6, OsGAMYB, OsHKT1;4, OsCTR3, and OsSUT1) and two newly identified genes (LOC_Os02g49700, LOC_Os03g28300) significantly associated with grain yield and its related traits under saline stress conditions were identified. These promising candidates provide valuable resources for validating potential ST-related genes and will facilitate rice breeding for salt tolerance through marker-assisted selection.

A new chicken 55K SNP genotyping array

BackgroundChina has the richest local chicken breeding resources in the world and is the world’s second largest producer of meat-type chickens. Development of a moderate-density SNP array for genetic analysis of chickens and breeding of meat-type chickens taking utility of those resources is urgently needed for conventional farms, breeding industry, and research areas.ResultsEight representative local breeds or commercial broiler lines with 3 pools of 48 individuals within each breed/line were sequenced and supplied the major SNPs resource. There were 7.09 million - 9.41 million SNPs detected in each breed/line. After filtering using multiple criteria such as preferred incorporation of trait-related SNPs and uniformity of distribution across the genome, 52.18 K SNPs were selected in the final array. It consists of: (i) 19.22 K SNPs from the genomes of yellow-feathered, cyan-shank partridge and white-feathered chickens; (ii) 5.98 K SNPs related to economic traits from the Illumina 60 K SNP Bead Chip, which were found as significant associated SNPs with 15 traits in a Beijing-You crossed Cobb F2 resource population by genome-wide association study analysis; (iii) 7.63 K SNPs from 861 candidate genes of economic traits; (iv) the 0.94 K SNPs related to residual feed intake; and (v) 18.41 K from chicken SNPdb. The polymorphisms of 9 extra local breeds and 3 commercial lines were examined with this array, and 40 K - 47 K SNPs were polymorphic (with minor allele frequency > 0.05) in those breeds. The MDS result showed that those breeds can be clearly distinguished by this newly developed genotyping array.ConclusionsWe successfully developed a 55K genotyping array by using SNPs segregated from typical local breeds and commercial lines. Compared to the existing Affy 600 K and Illumina 60 K arrays, there were 21,41 K new SNPs included on our Affy 55K array. The results of the 55K genotyping data can therefore be imputed to high-density SNPs genotyping data. The array offers a wide range of potential applications such as genomic selection breeding, GWAS of interested traits, and investigation of diversity of different chicken breeds.

Genome-wide association study of Mycobacterium avium subspecies Paratuberculosis infection in Chinese Holstein

BackgroundParatuberculosis is a contagious, chronic and enteric disease in ruminants, which is caused by Mycobacterium avium subspecies paratuberculosis (MAP) infection, resulting in enormous economic losses worldwide. There is currently no effective cure for MAP infection or a vaccine, it is thus important to explore the genetic variants that contribute to host susceptibility to infection by MAP, which may provide a better understanding of the mechanisms of paratuberculosis and benefit animal genetic improvement. Herein we performed a genome-wide association study (GWAS) to identify genomic regions and candidate genes associated with susceptibility to MAP infection in dairy cattle.ResultsUsing Illumina Bovine 50 K (54,609 SNPs) and GeneSeek HD (138,893 SNPs) chips, two analytical approaches were performed, GRAMMAR-GC and ROADTRIPS in 937 Chinese Holstein cows, among which individuals genotyped by the 50 K chip were imputed to HD SNPs with Beagle software. Consequently, 15 and 11 significant SNPs (P < 5 × 10− 5) were identified with GRAMMAR-GC and ROADTDRIPS, respectively. A total of 10 functional genes were in proximity to (i.e., within 1 Mb) these SNPs, including IL4, IL5, IL13, IRF1, MyD88, PACSIN1, DEF6, TDP2, ZAP70 and CSF2. Functional enrichment analysis showed that these genes were involved in immune related pathways, such as interleukin, T cell receptor signaling pathways and inflammatory bowel disease (IBD), implying their potential associations with susceptibility to MAP infection. In addition, by examining the publicly available cattle QTLdb, a previous QTL for MAP was found to be overlapped with one of regions detected currently at 32.5 Mb on BTA23, where the TDP2 gene was anchored.ConclusionsIn conclusion, we identified 26 SNPs located on 15 chromosomes in the Chinese Holstein population using two GWAS strategies with high density SNPs. Integrated analysis of GWAS, biological functions and the reported QTL information helps to detect positional candidate genes and the identification of regions associated with susceptibility to MAP traits in dairy cattle.