Genome-wide Simple Sequence Repeat Markers Research Articles

Development of Novel Genomewide Simple Sequence Repeat Markers for Acer truncatum Bunge and Assessment of Their Transferability to Other Closely Related Species

Acer truncatum Bunge is a versatile woody tree species with high economic and medicinal value in the production of bioactive substances and unsaturated fatty acids (especially nervonic acid). However, the exploitation and evaluation of A. truncatum germplasm resources are limited owing to a lack of sound molecular marker systems. In this study, a large set of genomewide simple sequence repeat (SSR) markers of A. truncatum was developed based on its whole-genome sequences. A total of 462,331 SSR loci were identified in the genome sequences, 99.3% (459,193) of which were located on 13 chromosomes. The chromosome length was significantly positively correlated with the number of SSR loci on the chromosome (r = 0.977, p < 0.001). The (A/T)n, (AT/TA)n, and (AAT/ATT/TAA/TTA/TAT/ATA)n were the most frequent motifs for mono-, di-, and trinucleotide repeat motifs, respectively, showing A/T-base bias. After BLASTN and electronic polymerase chain reaction (PCR) analyses, 199,990 loci with specific physical positions were screened. Most of the SSR loci were located in the intergenic regions and fewest in the coding sequences (CDSs). The frequency of loci with tri- and hexanucleotide repeat motifs was the highest in the CDSs, potentially serving to maintain the stability of gene function and structure. In randomly selected 105 SSR markers, 82 (78.1%) showed allelic polymorphism, with polymorphism information content (PIC) values of 0.032–0.926 (0.481 on average). The SSRs in the noncoding regions exhibited significantly higher PIC values than those in the CDSs. The transferability of the 105 markers was 48.6%–59.0% to seven other Acer species. The large set of valid SSR markers provides a powerful tool for studies on population genetics, conservation genetics, linkage mapping, comparative genomics, and marker-assisted breeding of the genus Acer.

Genome-wide simple sequence repeat markers in potato: abundance, distribution, composition, and polymorphism.

Simple sequence repeats (SSRs) are important sources of genetic diversity and are widely used as markers in genetics and molecular breeding. In this study, we examined four potato genomes of DM1-3 516 R44 (DM) from Solanum phureja, RH89039-16 (RH) from Solanum tuberosum, M6 from Solanum chacoense and Solanum commersonii to determine SSR abundance and distribution and develop a larger list of polymorphic markers for a potentially wide range of uses for the potato community. A total of 1,734,619 SSRs were identified across the four genomes with an average of 433,655 SSRs per genome and 2.31kb per SSR. The most abundant repeat units for mono-, di-, tri-, and tetra-nucleotide SSRs were (A/T)n, (AT/AT)n, (AAT/ATT)n, and (ATAT/ATAT)n, respectively. The SSRs were most abundant (78.79%) in intergenic regions and least abundant (3.68%) in untranslated regions. On average, 168,069 SSRs with unique flanking sequences were identified in the four genomes. Further, we identified 16,245 polymorphic SSR markers among the four genomes. Experimental validation confirmed 99.69% of tested markers could generate target bands. The high-density potato SSR markers developed in this study will undoubtedly facilitate the application of SSR markers for genetic research and marker-pyramiding in potato breeding.

Development and preliminary application of novel genomewide SSR markers for genetic diversity analysis of an economically important bio-control agent Platygaster robiniae (Hymenoptera: Platygastridae)

Platygaster robiniae Buhl and Duso (Hymenoptera: Platygastridae) is an egg-larvae parasitoid of the black locust gall midge (Obolodiplosis robiniae) (Haldeman) (Diptera: Cecidomyiidae) which is a serious invasive pest in China, where it attacks an important hardwood species, the black locust tree, Robini pseudoacacia L. (Fabales: Fabaceae). Despite the use of P. robiniae as an effective biocontrol agent, the absence of sequence data and other molecular markers have limited its genetic applications for pest management in forests. Simple-sequence repeats (SSRs) are valuable molecular markers for population genetic structure studies. In the present study, we identified 14,123 SSRs, of which 7799 SSR primer pairs were successfully designed. Subsequently, 240 SSR were chosen and tested with 48 P. robiniae accessions from two geographically separated populations in north and south China. Of these, 34 were polymorphic, with an average of three alleles (Na) and four genotypes (NG) each. The average values of observed heterozygosity (Ho) was 0.3514, expected heterozygosity (He) 0.4167, Shannon's information index (I) 0.7143, and polymorphism information content (PIC) 0.3558, respectively. Neighbour joining analysis (bootstrap 1000) revealed that Chengdu (CD) and Dangdong (DD) popluations clustered into two main divisions, and some individuals from two popluations clustered together as the third devision, which indicated the gene flow and genetic differentiation were present between two populations. Our finding indicates that these SSR markers will be useful for further studies on the genotype identification and genetic mapping of the genus Platygaster.

Development of Genome-wide Simple Sequence Repeat Markers from Whole-genome Sequence of Mungbean (Vigna radiata)

Background: Mungbean is an important pulse crop and it is mainly cultivated in Asia for human consumption. Its small genome and diploid nature make it a well-suited model organism among legume crops. Thus, cost-effective, reliable and highly polymorphic molecular markers distributing the whole genome are needed for diversity, mapping and functional genomics studies in this model species. Methods: The whole-genome sequence of mungbean was obtained and used as a source of identification of simple sequence repeats (SSR). The sequence reads were aligned and SSRs detection was performed using the Phobos plugin tandem repeat finder in the Geneious software program. A total of 12 mungbean genotypes were selected to validate the newly developed SSR markers. Result: In the present study, a total of 12, 49,774 and 11, 86, 386 perfect and imperfect SSR repeats were identified from the mungbean genome. The tri-repeats were the most abundant (26.10%), followed by hexa (20.82%), penta (20.45%), tetra (17.65%) and di-repeats (14.95%). We designed 1330 SSR primers based on the genomic sequence of flanking perfect SSRs (Di and tri-repeats). Among them, 50 SSR primers uniformly distributed across the 11 mungbean chromosomes were selected and used to validate 12 mungbean genotypes. The newly developed genomic SSR markers generated in the present study are a valuable genomic resource for the mungbean breeding programs.

Development of high conserved cross-species microsatellite markers from cucumber genome and their applicability in genetic diversity and comparative mapping

One of the most widely applicable and used markers considered in plant research is simple sequence repeats (SSRs). The Gy14 cucumber genome provided information for the development of SSR marker in this species which might be used in other related species additionally. We, therefore, developed genome-wide SSR markers from cucumber, which were used for genetic diversity analysis in 16 different cucurbits species and comparative mapping with melon and watermelon. A total of 2171 SSR motifs were identified from seven cucumber chromosomes. Out of them, 1749 markers belong to melon while 442 markers to watermelon. We experimentally validated 70 SSR markers to check their cross-species transferability among 16 different cucurbits species belongs to six genera. Maximum% polymorphism has been recorded for Momordica charantia (82%) followed by Momordica cochinchinesis (78.18%) and Luffa harmaphrodita (73.68%) while Benincasa hispida (49.21%) exhibited minimum% polymorphism. The large number of cucumber SSR markers developed in the present study provides a valuable resource for genetic linkage map construction, molecular mapping, and marker-assisted selection (MAS) in cucumber. Furthermore, the cross-species transferable SSR markers could also be useful in various molecular markers related studies in other closely related species in the Cucurbitaceae family in which draft genomes are not yet available.

Marker Assisted Development and Characterization of Herbicide Tolerant Near Isogenic Lines of a Mega Basmati Rice Variety, \u201cPusa Basmati 1121\u201d

BackgroundDirect-seeded rice (DSR) is a potential technology for sustainable rice farming as it saves water and labor. However, higher incidence of weed under DSR limits productivity. Therefore, there is a need to develop herbicide tolerant (HT) rice varieties.ResultsWe used marker assisted backcross breeding (MABB) to transfer a mutant allele of Acetohydroxy acid synthase (AHAS) gene, which confers tolerance to imidazolinone group of herbicides from the donor parent (DP) “Robin” into the genetic background of an elite popular Basmati rice variety, Pusa Basmati 1121 (PB 1121). Foreground selection was done using the AHAS gene linked Simple Sequence Repeat (SSR) marker RM6844 and background selection was performed using 112 genome-wide SSR markers polymorphic between PB 1121 and Robin. Phenotypic selection for agronomic, Basmati grain and cooking quality traits in each generation was carried out to improve the recovery of recurrent parent phenome (RPP). Finally, a set of 12 BC4F4 near isogenic lines (NILs), with recurrent parent genome (RPG) recovery ranging from 98.66 to 99.55% were developed and evaluated. PB 1121-HT NILs namely 1979-14-7-33-99-10, 1979-14-7-33-99-15 and 1979-14-7-33-99-66 were found superior to PB 1121 in yield with comparable grain and cooking quality traits and herbicide tolerance similar to Robin.ConclusionOverall, the present study reports successful development of HT NILs in the genetic background of popular Basmati rice variety, PB 1121 by introgression of mutated AHAS allele. This is the first report on the development of HT Basmati rice. Superior NILs are being evaluated in the national Basmati trials, the release of which is likely to provide a viable option for the adoption of DSR technology in Basmati rice cultivation.

Development of a Large Gene-Associated SSR Marker Set and in-Depth Genetic Characterization in Scarlet Sage.

Salvia splendens, scarlet or tropical sage, is a tender perennial herbaceous flowering plant popularly grown in public and private gardens all over the world. In this study, we developed a set of simple sequence repeats (SSRs) from genome-wide sequences to assess the genetic diversity and population structure among 112 cultivars. We obtained 364,379 SSRs by mining scarlet sage’s recently published whole genome sequence; 14,545 gene-associated SSR loci were identified in 2 kb gene flanking regions. Among the 768 gene-associated SSR primer sets we screened, 576 loci successfully amplified in DNA pools of 3–4 different cultivars, of which 271 remained polymorphic when tested across eight individual plants. We searched for the related gene functions attributable to these gene-associated SSRs using diverse databases, resulting in 259 Non-redundant matching sequences, 205 individual Gene Ontology (GO) terms, 236 assigned to eukaryotic orthologous groups, and 67 KEGG-annotated (Kyoto Encyclopedia of Genes and Genomes) sequences. We finally selected 41 polymorphic SSR loci to infer genetic diversity and population structure among 112 S. splendens accessions. Based on the developed gene-associated SSRs, clustering analyses consistently revealed two distinct genetic groups within the core collection of S. splendens cultivars. This work developed and characterized an exhaustive set of genome-wide gene-associated SSR markers for scarlet sage. These SSRs can provide species identification, genetic diversity and population structure information for S. splendens, and will therefore be important tools for the management and protection of S. splendens germplasm.

Genome-Wide SSR 마커를 이용한 주요 산지별 참당귀의 유전다양성 분석

Background: Angelica gigas Nakai has been used as an herbal medicine in Eastern Asia for treating disorders in women for a long time. To date there are no studies on the genetic diversity of A. gigas. The present study aimed to study the genetic diversity of A. gigas variants using genomewide simple sequence repeat (SSR) markers.BRMethods and Results: The genetic diversity of 199 variants of A. gigas cultivated in of different regions, was analyzed using 5 genome-wide SSR markers. The results revealed that the genetic variants were very diverse, and genetic analysis using the 5 SSR markers revealed high diversity among the variants.BRConclusions: It is expected that the development of the true Angleical cultivar, by studying the system and group selection, can be achieved by genetic analysis using the developed markers, for generating a genetically fixed lineage and group selection.

Classification of interspecific and intraspecific species by genome-wide SSR markers on Dendrobium

Dendrobium is a threatened and valuable genus in orchids. Many of them were common in medicinal and ornamental markets. In this study, a total of 198,990 simple sequence repeats (SSR) were identified from 3814 genomic scaffolds in D. catenatum (180 SSRs/Mb). Dinucleotide, trinucleotide and tetra-nucleotide covered about 0.2428%, 0.0544% and 0.0039% to the whole genome, separately. AT and TA, AAT and TGT, AAAT and TTTA were the corresponded dominant motifs. Total repetition of A and T was significantly greater than that of C and G. Moreover, 100 locus-specific primer pairs were randomly selected. And 73 of them produced polymorphic products in interspecific identification of 37 Dendrobium species. The interspecific effective polymorphic bands (EPBs), polymorphism information content (PIC), genetic diversity (Ht), genetic differentiation (Gst) and gene flow (Nm) of the novel SSR markers were 9.68, 0.528, 0.375, 0.499 and 0.753. The affinity of species and its varietas was confirmed in the phylogenetic tree. Additionally, 23, 25 and 12 SSR markers showed efficacy in intraspecific identification of 32 individuals in D. catenatum, 32 individuals in D. denneanum and 64 individuals in D. nobile, respectively. This confirmed the suitable transferability of SSR markers in cross-species. The intraspecific EPBs, PIC, Ht, Gst and Nm were 3.95, 0.554, 0.626, 0.226 and 2.305. The phylogenetic subgroups were significantly associated with plant height, epidermis and flower color. The electrophoretograms were clear for observation and suitable for auto-genotyping. The releasing of much more genome-wide SSR markers would be valuable for genetic studies and molecular breeding in Dendrobium.

QTL mapping of fruit nutritional and flavor components in tomato (Solanum lycopersicum) using genome-wide SSR markers and recombinant inbred lines (RILs) from an intra-specific cross

Fruit nutritional and flavor components are important targets for breeding new cultivars of tomato (Solanum lycopersicum L.). We developed 108 recombinant inbred lines (the K39 RILs) in the F6 generation from a cross between two phenotypically different breeding lines, K03 and K09. A linkage map was constructed using 172 genome-wide simple sequence repeat markers, 3 single-nucleotide polymorphism markers, and 2 phenotypic markers. The K39 RIL map consists of 12 linkage groups (LGs) and covers a genetic distance of 1089 cM. We measured the fruit soluble solids content (SSC), titratable acidity (TA), glutamic acid content (GLU), and lycopene content (LYC) of each line in four generations (F6, F8, F10, F11), β-carotene content (CAR) in two generations, and pH in one generation. By composite interval mapping that considered yearly variations in components as non-genetic effects, we detected three quantitative trait loci (QTLs) for SSC, four for TA, two for CAR, and one each for GLU, LYC, and pH. Among them, we found two QTLs for TA in LGs 6 and 11, those for GLU and LYC were candidates for novel QTLs. QTLs detected in this study were clustered in five LGs, but we observed no apparent trade-off relationships among the QTLs in each LG. Being derived from an intra-specific cross of tomato breeding materials, these QTLs can be used in practical breeding for improving fruit quality with low risk of linkage drag.

Microsatellite mining in the genus Colletotrichum

Genomic data available in the public database are valuable resources for mining microsatellite or simple sequence repeat (SSR) markers. Though microsatellite markers are available for a few Colletotrichum species but their meagre number and species specificity warrants additional search in the publicly available genome databases. Therefore, in the present investigation, eight Colletotrichum genomes belonging to six clades were mined for microsatellites and we developed 57,170 microsatellite markers. Di and tri microsatellite motifs accounted for >80% share while tetra to deca motifs were rare. Ninety-nine percent of the microsatellites produced a single amplicion when subjected to electronic PCR. In silico cross transferability of the microsatellites exhibited specificity to respective species, illustrating the conserved sequences flanking the microsatellite regions. We found maximum microsatellite cross transferability among C. acutatum, C. fioriniae, and C. nymphaeae genomes that belong to acutatum clade. Thus suggesting that the microsatellites developed for one species in a genome clade may amplify other species of same clade. PCR amplification of 150 microsatellite markers confirms the locus specific amplification. Among the 110 microsatellites used for genotyping the 14 diverse races of C. lindemuthianum, 100 markers were polymorphic. Genotyping of 14 diverse bean anthracnose races with 50 SSR markers grouped them as per their geographic location. We report microsatellite markers for eight Colletotrichum genomes that belong to six clades and this is the first study of genome wide microsatellite marker development in the genus. These genome wide SSR markers will provide a useful tool to discover the population structure in Colletotrichum species and evolutionary insights in future.

Development of Genome-Wide SSR Markers from Angelica gigas Nakai Using Next Generation Sequencing.

Angelica gigas Nakai is an important medicinal herb, widely utilized in Asian countries especially in Korea, Japan, and China. Although it is a vital medicinal herb, the lack of sequencing data and efficient molecular markers has limited the application of a genetic approach for horticultural improvements. Simple sequence repeats (SSRs) are universally accepted molecular markers for population structure study. In this study, we found over 130,000 SSRs, ranging from di- to deca-nucleotide motifs, using the genome sequence of Manchu variety (MV) of A. gigas, derived from next generation sequencing (NGS). From the putative SSR regions identified, a total of 16,496 primer sets were successfully designed. Among them, we selected 848 SSR markers that showed polymorphism from in silico analysis and contained tri- to hexa-nucleotide motifs. We tested 36 SSR primer sets for polymorphism in 16 A. gigas accessions. The average polymorphism information content (PIC) was 0.69; the average observed heterozygosity (HO) values, and the expected heterozygosity (HE) values were 0.53 and 0.73, respectively. These newly developed SSR markers would be useful tools for molecular genetics, genotype identification, genetic mapping, molecular breeding, and studying species relationships of the Angelica genus.

Development of genome-wide SSR markers in horsegram and their use for genetic diversity and cross-transferability analysis

Horsegram [Macrotyloma uniflorum (Lam.) Verdc.] commonly known as kulthi or Madras gram is an important drought tolerant legume crop used as food and fodder in India and across the globe. Horsegram is tolerant to many biotic and abiotic stresses and considered a potential future food legume. Despite being a multiutility crop, insufficient genomic information is available in this species, which is otherwise required for genetic improvement. Hence, in the present work we used next-generation sequencing (NGS) technology for genome-wide development and characterization of novel simple sequence repeat (SSR) markers in horsegram. In all, 2458 SSR primer pairs were designed from NGS data and 117 SSRs were characterized in 48 diverse lines of horsegram. Cross-transferability of these markers was also checked in nine related legume species. The polymorphic SSRs revealed high diversity measures such as mean values of expected heterozygosity (He; 0.54), observed heterozygosity (Ho; 0.64), and polymorphism information content (PIC; 0.46). Analysis of molecular variance (AMOVA) revealed high degree of genetic variance within the populations. Dendrogram based on Jaccard’s similarity coefficient and principal component analysis (PCA) revealed two groups in the analyzed accessions. This observation was further confirmed by Bayesian genetic STRUCTURE analysis. The SSR markers developed herein can be used in diverse genetic analysis including association mapping in this crop and also in related legume crops with limited marker resources. Hence, this new SSR dataset can be useful for molecular breeding research in this underutilized pulse crop. In addition, genetic diversity estimates of analyzed germplasm can be important for devising future breeding programmes in horsegram.

Genome-wide assessment of population structure, linkage disequilibrium and resistant QTLs in Chinese wild grapevine

Chinese wild grapevine is an important germplasm source worldwide; thus, it is necessary to study its genetic diversity, population structure, and linkage disequilibrium (LD). In this study, 81 strains of Chinese wild grapevine were studied and constituted the core collection. These strains were genotyped according to 160 genome-wide SSR (simple sequence repeat) markers. All SSR markers were widely spread across the strains and revealed a total of 3469 alleles. After population structure analysis, all the Chinese wild grapevine strains were grouped into two subgroups that were well matched with the geographical distribution and the results published by our research team. Of all SSR pairs, 8.3% (P<0.01) were in LD. For all inner chromosomal loci pairs, the mean r2 value was 0.0229. The LD decay distance across Chinese wild grapevine was up to 14.13cM, below the critical r2 value of 0.1, following y=−0.0383 ln (x)+0.2016. According to both the linear mixed model and general linear model, the associations of the 160 SSR markers with grape white rot resistance were calculated. Five associated markers were located, four of which had been previously associated with other resistance traits and one of which was new. Chinese wild grapevine association mapping was performed to anchor useful quantitative trait loci (QTLs), and the five markers identified can help us anchor additional resistance-associated genes.

Development of genome-wide SSR markers in melon with their cross-species transferability analysis and utilization in genetic diversity study

Simple sequence repeats (SSRs) are one of the most informative and widely used molecular markers in plant research. The melon draft genome has provided a powerful tool for SSR marker development in this species in which there are still not enough SSR markers. We therefore developed genome-wide SSR markers from melon, which were used for genetic diversity analysis in melon accessions and comparative mapping with cucumber and watermelon. A total of 44,265 microsatellites from the melon genome were characterized, of which 28,570 SSR markers were developed. In silico PCR analysis with these SSR markers identified 4002 and 1085 with one amplicon in cucumber and watermelon genome, respectively. With these cross-species transferable melon SSR markers, the chromosome synteny between melon and cucumber as well as watermelon was established, which revealed complicated mosaic patterns of syntenic blocks among them. We experimentally validated 384 SSR markers, from which 42 highly informative SSR ones were selected for genetic diversity and population structure analysis among 118 melon accessions. The large number of melon SSR markers developed in this study provides a valuable resource for genetic linkage map construction, molecular mapping, and marker-assisted selection (MAS) in melon. Furthermore, the cross-species transferable SSR markers could also be useful in various molecular marker-related studies in other closely related species in Cucurbitaceae family in which draft genomes are not yet available.

An Efficient Strategy Combining SSR Markers- and Advanced QTL-seq-driven QTL Mapping Unravels Candidate Genes Regulating Grain Weight in Rice.

Development and use of genome-wide informative simple sequence repeat (SSR) markers and novel integrated genomic strategies are vital to drive genomics-assisted breeding applications and for efficient dissection of quantitative trait loci (QTLs) underlying complex traits in rice. The present study developed 6244 genome-wide informative SSR markers exhibiting in silico fragment length polymorphism based on repeat-unit variations among genomic sequences of 11 indica, japonica, aus, and wild rice accessions. These markers were mapped on diverse coding and non-coding sequence components of known cloned/candidate genes annotated from 12 chromosomes and revealed a much higher amplification (97%) and polymorphic potential (88%) along with wider genetic/functional diversity level (16–74% with a mean 53%) especially among accessions belonging to indica cultivar group, suggesting their utility in large-scale genomics-assisted breeding applications in rice. A high-density 3791 SSR markers-anchored genetic linkage map (IR 64 × Sonasal) spanning 2060 cM total map-length with an average inter-marker distance of 0.54 cM was generated. This reference genetic map identified six major genomic regions harboring robust QTLs (31% combined phenotypic variation explained with a 5.7–8.7 LOD) governing grain weight on six rice chromosomes. One strong grain weight major QTL region (OsqGW5.1) was narrowed-down by integrating traditional QTL mapping with high-resolution QTL region-specific integrated SSR and single nucleotide polymorphism markers-based QTL-seq analysis and differential expression profiling. This led us to delineate two natural allelic variants in two known cis-regulatory elements (RAV1AAT and CARGCW8GAT) of glycosyl hydrolase and serine carboxypeptidase genes exhibiting pronounced seed-specific differential regulation in low (Sonasal) and high (IR 64) grain weight mapping parental accessions. Our genome-wide SSR marker resource (polymorphic within/between diverse cultivar groups) and integrated genomic strategy can efficiently scan functionally relevant potential molecular tags (markers, candidate genes and alleles) regulating complex agronomic traits (grain weight) and expedite marker-assisted genetic enhancement in rice.

Genome scans for divergent selection in natural populations of the widespread hardwood species Eucalyptus grandis (Myrtaceae) using microsatellites.

Identification of loci or genes under natural selection is important for both understanding the genetic basis of local adaptation and practical applications, and genome scans provide a powerful means for such identification purposes. In this study, genome-wide simple sequence repeats markers (SSRs) were used to scan for molecular footprints of divergent selection in Eucalyptus grandis, a hardwood species occurring widely in costal areas from 32° S to 16° S in Australia. High population diversity levels and weak population structure were detected with putatively neutral genomic SSRs. Using three FST outlier detection methods, a total of 58 outlying SSRs were collectively identified as loci under divergent selection against three non-correlated climatic variables, namely, mean annual temperature, isothermality and annual precipitation. Using a spatial analysis method, nine significant associations were revealed between FST outlier allele frequencies and climatic variables, involving seven alleles from five SSR loci. Of the five significant SSRs, two (EUCeSSR1044 and Embra394) contained alleles of putative genes with known functional importance for response to climatic factors. Our study presents critical information on the population diversity and structure of the important woody species E. grandis and provides insight into the adaptive responses of perennial trees to climatic variations.

Accuracy of genomic selection in biparental populations of flax (Linum usitatissimum L.)

Flax is an important economic crop for seed oil and stem fiber. Phenotyping of traits such as seed yield, seed quality, stem fiber yield, and quality characteristics is expensive and time consuming. Genomic selection (GS) refers to a breeding approach aimed at selecting preferred individuals based on genomic estimated breeding values predicted by a statistical model based on the relationship between phenotypes and genome-wide genetic markers. We evaluated the prediction accuracy of GS (rMP) and the efficiency of GS relative to phenotypic selection (RE) for three GS models: ridge regression best linear unbiased prediction (RR-BLUP), Bayesian LASSO (BL), and Bayesian ridge regression (BRR), for seed yield, oil content, iodine value, linoleic, and linolenic acid content with a full and a common set of genome-wide simple sequence repeat markers in each of three biparental populations. The three GS models generated similar rMP and RE, while BRR displayed a higher coefficient of determination (R2) of the fitted models than did RR-BLUP or BL. The mean rMP and RE varied for traits with different heritabilities and was affected by the genetic variation of the traits in the populations. GS for seed yield generated a mean RE of 1.52 across populations and marker sets, a value significantly superior to that for direct phenotypic selection. Our empirical results provide the first validation of GS in flax and demonstrate that GS could increase genetic gain per unit time for linseed breeding. Further studies for selection of training populations and markers are warranted.

Geography and end use drive the diversification of worldwide winter rye populations.

To meet the current challenges in human food production, improved understanding of the genetic diversity of crop species that maximizes the selection efficacy in breeding programs is needed. The present study offers new insights into the diversity, genetic structure and demographic history of cultivated rye (Secale cereale L.). We genotyped 620 individuals from 14 global rye populations with a different end use (grain or forage) at 32 genome-wide simple sequence repeat markers. We reveal the relationships among these populations, their sizes and the timing of domestication events using population genetics and model-based inference with approximate Bayesian computation. Our main results demonstrate (i) a high within-population variation and genetic diversity, (ii) an unexpected absence of reduction in diversity with an increasing improvement level and (iii) patterns suggestive of multiple domestication events. We suggest that the main drivers of diversification of winter rye are the end use of rye in two early regions of cultivation: rye forage in the Mediterranean area and grain in northeast Europe. The lower diversity and stronger differentiation of eastern European populations were most likely due to more intensive cultivation and breeding of rye in this region, in contrast to the Mediterranean region where it was considered a secondary crop or even a weed. We discuss the relevance of our results for the management of gene bank resources and the pitfalls of inference methods applied to crop domestication due to violation of model assumptions and model complexity.

Genome-wide mining, characterization, and development of microsatellite markers in Marsupenaeus japonicus by genome survey sequencing

The kuruma prawn, Marsupenaeus japonicus, is one of the most cultivated and consumed species of shrimp. However, very few molecular genetic/genomic resources are publically available for it. Thus, the characterization and distribution of simple sequence repeats (SSRs) remains ambiguous and the use of SSR markers in genomic studies and marker-assisted selection is limited. The goal of this study is to characterize and develop genome-wide SSR markers in M. japonicus by genome survey sequencing for application in comparative genomics and breeding. A total of 326 945 perfect SSRs were identified, among which dinucleotide repeats were the most frequent class (44.08%), followed by mononucleotides (29.67%), trinucleotides (18.96%), tetranucleotides (5.66%), hexanucleotides (1.07%), and pentanucleotides (0.56%). In total, 151 541 SSR loci primers were successfully designed. A subset of 30 SSR primer pairs were synthesized and tested in 42 individuals from a wild population, of which 27 loci (90.0%) were successfully amplified with specific products and 24 (80.0%) were polymorphic. For the amplified polymorphic loci, the alleles ranged from 5 to 17 (with an average of 9.63), and the average PIC value was 0.796. A total of 58 256 SSR-containing sequences had significant Gene Ontology annotation; these are good functional molecular marker candidates for association studies and comparative genomic analysis. The newly identified SSRs significantly contribute to the M. japonicus genomic resources and will facilitate a number of genetic and genomic studies, including high density linkage mapping, genome-wide association analysis, marker-aided selection, comparative genomics analysis, population genetics, and evolution.