Segregation Distortion Research Articles

Identification of loci associated with embryo yield in microspore culture of Brassica rapa by segregation distortion analysis.

We identified three physical positions associated with embryo yield in microspore culture of Brassica rapa by segregation distortion analysis. We also confirmed their genetic effects on the embryo yield. Isolated microspore culture is well utilized for the production of haploid or doubled-haploid plants in Brassica crops. Brassica rapa cv. 'Ho Mei' is one of the most excellent cultivars in embryo yield of microspore culture. To identify the loci associated with microspore embryogenesis, segregation analysis of 154 DNA markers anchored to B. rapa chromosomes (A01-A10) was performed using a population of microspore-derived embryos obtained from an F1 hybrid between 'CR-Seiga', a low yield cultivar in microspore-derived embryos, and 'Ho Mei'. Three regions showing significant segregation distortion with increasing 'Ho Mei' alleles were detected on A05, A08 and A09, although these regions showed the expected Mendelian segregation ratio in an F2 population. The additive effect of alleles in these regions on embryo yield was confirmed in a BC3F1 population. One region on A08 containing Br071-5c had a higher effect than the other regions. Polymorphism of nucleotide sequences around the Br071-5c locus was investigated to find the gene possibly responsible for efficient embryogenesis from microspores.

Development of retrotransposon-based molecular markers and their application in genetic mapping in chokecherry (Prunus virginiana L.)

Retrotransposons are the largest group of transposable elements (TEs) that are ubiquitous and well dispersed in plant genomes. Transposition/insertion of TEs on chromosomes often generates unique repeat junctions (RJs) between TEs and their flanking sequences. Long terminal repeats (LTR) are well conserved and abundant in plant genomes, making LTR retrotransposons valuable for development of TE junction-based markers. In this study, LTR retrotransposons and their RJs were detected from chokecherry genome sequences generated by Roche 454 sequencing. A total of 1246 LTR retrotransposons were identified, and 338 polymerase chain reaction primer pairs were designed. Of those, 336 were used to amplify DNA from chokecherry and other rosaceous species. An average of 283 of 336 (84.2 %) LTR primer pairs effectively amplified DNA from chokecherries. One hundred and seventeen chokecherry LTR primers also produced amplification in other Prunus (99) or rosaceous species (19). A total of 59 of 78 polymorphic LTR markers were qualified for linkage map construction according to the segregation distortion Chi-square (χ 2) test. Forty-eight LTR markers were successfully located on a previously constructed chokecherry map. The majority of the LTR markers were mapped on LG XI of the chokecherry map. Our results suggest that LTR marker development using random genome sequences is rapid and cost-efficient. Confirmed applicability of LTR markers in map construction and genetic mapping will facilitate genetic research in chokecherry and other rosaceous species.

Analysis of recombination QTLs, segregation distortion, and epistasis for fitness in maize multiple populations using ultra-high-density markers.

Using two nested association mapping populations and high-density markers, some important genomic regions controlling recombination frequency and segregation distortion were detected. Understanding the maize genomic features would be useful for the study of genetic diversity and evolution and for maize breeding. Here, we used two maize nested association mapping (NAM) populations separately derived in China (CN-NAM) and the US (US-NAM) to explore the maize genomic features. The two populations containing 36 families and about 7000 recombinant inbred lines were evaluated with genotyping-by-sequencing. Through the comparison between the two NAMs, we revealed that segregation distortion is little, whereas epistasis for fitness is present in the two maize NAM populations. When conducting quantitative trait loci (QTL) mapping for the total number of recombination events, we detected 14 QTLs controlling recombination. Using high-density markers to identify segregation distortion regions (SDRs), a total of 445 SDRs were detected within the 36 families, among which 15 common SDRs were found in at least ten families. About 80% of the known maize gametophytic factors (ga) genes controlling segregation distortion were overlapped with highly significant SDRs. In addition, we also found that the regions with high recombination rate and high gene density usually tended to have little segregation distortion. This study will facilitate population genetic studies and gene cloning affecting recombination variation and segregation distortion in maize, which can improve plant breeding progress.

Genomic Conflicts that Cause Pollen Mortality and Raise Reproductive Barriers in Arabidopsis thaliana.

Species differentiation and the underlying genetics of reproductive isolation are central topics in evolutionary biology. Hybrid sterility is one kind of reproductive barrier that can lead to differentiation between species. Here, we analyze the complex genetic basis of the intraspecific hybrid male sterility that occurs in the offspring of two distant natural strains of Arabidopsis thaliana, Shahdara and Mr-0, with Shahdara as the female parent. Using both classical and quantitative genetic approaches as well as cytological observation of pollen viability, we demonstrate that this particular hybrid sterility results from two causes of pollen mortality. First, the Shahdara cytoplasm induces gametophytic cytoplasmic male sterility (CMS) controlled by several nuclear loci. Second, several segregation distorters leading to allele-specific pollen abortion (pollen killers) operate in hybrids with either cytoplasm. The complete sterility of the hybrid with the Shahdara cytoplasm results from the genetic linkage of the two causes of pollen mortality, i.e., CMS nuclear determinants and pollen killers. Furthermore, natural variation at these loci in A. thaliana is associated with different male-sterility phenotypes in intraspecific hybrids. Our results suggest that the genomic conflicts that underlie segregation distorters and CMS can concurrently lead to reproductive barriers between distant strains within a species. This study provides a new framework for identifying molecular mechanisms and the evolutionary history of loci that contribute to reproductive isolation, and possibly to speciation. It also suggests that two types of genomic conflicts, CMS and segregation distorters, may coevolve in natural populations.

SNP-Based QTL Mapping of 15 Complex Traits in Barley under Rain-Fed and Well-Watered Conditions by a Mixed Modeling Approach.

This study identified single nucleotide polymorphism (SNP) markers associated with 15 complex traits in a breeding population of barley (Hordeum vulgare L.) consisting of 137 recombinant chromosome substitution lines (RCSL), evaluated under contrasting water availability conditions in the Mediterranean climatic region of central Chile. Given that markers showed a very strong segregation distortion, a quantitative trait locus/loci (QTL) mapping mixed model was used to account for the heterogeneity in genetic relatedness between genotypes. Fifty-seven QTL were detected under rain-fed conditions, which accounted for 5–22% of the phenotypic variation. In full irrigation conditions, 84 SNPs were significantly associated with the traits studied, explaining 5–35% of phenotypic variation. Most of the QTL were co-localized on chromosomes 2H and 3H. Environment-specific genomic regions were detected for 12 of the 15 traits scored. Although most QTL-trait associations were environment and trait specific, some important and stable associations were also detected. In full irrigation conditions, a relatively major genomic region was found underlying hectoliter weight (HW), on chromosome 1H, which explained between 27% (SNP 2711-234) and 35% (SNP 1923-265) of the phenotypic variation. Interestingly, the locus 1923-265 was also detected for grain yield at both environmental conditions, accounting for 9 and 18%, in the rain-fed and irrigation conditions, respectively. Analysis of QTL in this breeding population identified significant genomic regions that can be used for marker-assisted selection (MAS) of barley in areas where drought is a significant constraint.

Exploring the genetic characteristics of 93-11 and Nipponbare recombination inbred lines based on the GoldenGate SNP assay.

Understanding genetic characteristics in rice populations will facilitate exploring evolutionary mechanisms and gene cloning. Numerous molecular markers have been utilized in linkage map construction and quantitative trait locus (QTL) mappings. However, segregation-distorted markers were rarely considered, which prevented understanding genetic characteristics in many populations. In this study, we designed a 384-marker GoldenGate SNP array to genotype 283 recombination inbred lines (RILs) derived from 93-11 and Nipponbare Oryza sativa crosses. Using 294 markers that were highly polymorphic between parents, a linkage map with a total genetic distance of 1,583.2 cM was constructed, including 231 segregation-distorted markers. This linkage map was consistent with maps generated by other methods in previous studies. In total, 85 significant quantitative trait loci (QTLs) with phenotypic variation explained (PVE) values≥5% were identified. Among them, 34 QTLs were overlapped with reported genes/QTLs relevant to corresponding traits, and 17 QTLs were overlapped with reported sterility-related genes/QTLs. Our study provides evidence that segregation-distorted markers can be used in linkage map construction and QTL mapping. Moreover, genetic information resulting from this study will help us to understand recombination events and segregation distortion. Furthermore, this study will facilitate gene cloning and understanding mechanism of inter-subspecies hybrid sterility and correlations with important agronomic traits in rice.

Exploiting genotyping by sequencing to characterize the genomic structure of the American cranberry through high-density linkage mapping.

BackgroundThe application of genotyping by sequencing (GBS) approaches, combined with data imputation methodologies, is narrowing the genetic knowledge gap between major and understudied, minor crops. GBS is an excellent tool to characterize the genomic structure of recently domesticated (~200 years) and understudied species, such as cranberry (Vaccinium macrocarpon Ait.), by generating large numbers of markers for genomic studies such as genetic mapping.ResultsWe identified 10842 potentially mappable single nucleotide polymorphisms (SNPs) in a cranberry pseudo-testcross population wherein 5477 SNPs and 211 short sequence repeats (SSRs) were used to construct a high density linkage map in cranberry of which a total of 4849 markers were mapped. Recombination frequency, linkage disequilibrium (LD), and segregation distortion at the genomic level in the parental and integrated linkage maps were characterized for first time in cranberry. SSR markers, used as the backbone in the map, revealed high collinearity with previously published linkage maps. The 4849 point map consisted of twelve linkage groups spanning 1112 cM, which anchored 2381 nuclear scaffolds accounting for ~13 Mb of the estimated 470 Mb cranberry genome. Bin mapping identified 592 and 672 unique bins in the parentals and a total of 1676 unique marker positions in the integrated map. Synteny analyses comparing the order of anchored cranberry scaffolds to their homologous positions in kiwifruit, grape, and coffee genomes provided initial evidence of homology between cranberry and closely related species.ConclusionsGBS data was used to rapidly saturate the cranberry genome with markers in a pseudo-testcross population. Collinearity between the present saturated genetic map and previous cranberry SSR maps suggests that the SNP locations represent accurate marker order and chromosome structure of the cranberry genome. SNPs greatly improved current marker genome coverage, which allowed for genome-wide structure investigations such as segregation distortion, recombination, linkage disequilibrium, and synteny analyses. In the future, GBS can be used to accelerate cranberry molecular breeding through QTL mapping and genome-wide association studies (GWAS).Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-2802-3) contains supplementary material, which is available to authorized users.

Marker assisted backcross breeding of Bg 358 (<em>Oryza sativa</em> L.) for the anaerobic germination tolerant QTL <em>AG1</em>

Sustainability of transplanting systems for rice crop establishment in Sri Lanka is threatened due to climatic changes and heavy rains. Tolerance to anaerobic germination (AG) stress is a key trait that will ensure good crop establishment in direct seeded rice (DSR) farming systems. In this study Marker Assisted backcross breeding was carried out to transfer the quantitative trait loci - QTL AG1 (qAG-9-2), in to the local variety Bg 358 for the development of AG stress tolerant elite lines by AG1 donors IR64-AG1 and Ciherang-Sub1AG1. Marker assisted selection (MAS) was carried out through foreground and recombinant selection. Molecular marker optimization for RM24161, RM8300 and RM553 to the QTL AG1 was carried out using BC1F1 populations. DNA was extracted and PCR was performed using simple sequence repeat (SSR) markers and visualized on 2.5% agarose gel. Based on polymorphism exhibited, RM24161 was chosen as the foreground selection marker, RM553 and RM8300 chosen as proximal and distal markers for recombinant selection. It was suggestive through this study to choose flanking markers RM105 & RM219, closer to the qAG-9-2 locus for recombinant selection as the selected recombinant makers were ineffective and exhibited marker segregation distortion. RM24161 was found to be a tightly linked marker to the AG tolerant QTL AG1 (qAG-9-2) and was successfully used for selection of lines by MAS in generation of anaerobic germination tolerant elite lines.

Generalizing Contextual Analysis.

Okasha, in Evolution and the Levels of Selection, convincingly argues that two rival statistical decompositions of covariance, namely contextual analysis and the neighbour approach, are better causal decompositions than the hierarchical Price approach. However, he claims that this result cannot be generalized in the special case of soft selection and argues that the Price approach represents in this case a better option. He provides several arguments to substantiate this claim. In this paper, I demonstrate that these arguments are flawed and argue that neither the Price equation nor the contextual and neighbour partitionings sensu Okasha are adequate causal decompositions in cases of soft selection. The Price partitioning is generally unable to detect cross-level by-products and this naturally also applies to soft selection. Both contextual and neighbour partitionings violate the fundamental principle of determinism that the same cause always produces the same effect. I argue that a fourth partitioning widely used in the contemporary social sciences, under the generic term of 'hierarchical linear model' and related to contextual analysis understood broadly, addresses the shortcomings of the three other partitionings and thus represents a better causal decomposition. I then defend this model against the argument that because it predicts that there is some organismal selection in some specific cases of segregation distortion then it should be rejected. I show that cases of segregation distortion that intuitively seem to contradict the conclusion drawn from the hierarchical linear model are in fact cases of multilevel selection 2 while the assessment of the different partitionings are restricted to multilevel selection 1.

Characterization of a Segregation Distortion Locus with Powdery Mildew Resistance in a Wheat-Thinopyrum intermedium Introgression Line WE99.

Exploitation of host resistance is important for controlling powdery mildew of wheat (Triticum aestivum L.). In this study, a wheat-Thinopyrum intermedium introgression line, designated WE99, conferred seedling resistance to 47 of 49 Blumeria graminis f. sp. tritici isolates. Genetic analysis demonstrated that the resistance segregation deviated significantly from a single gene Mendelian ratio. However, marker analysis indicated that only a single recessive resistance gene, temporarily designated PmWE99, conferred powdery mildew resistance (Pm). PmWE99 was mapped to chromosome arm 2BS and linked to the three simple-sequence repeat markers Gwm148, Gwm271, and Barc55. Using race spectrum analysis, PmWE99 was shown to be significantly different from the documented genes Pm42 and MlIW170 located on chromosome arm 2BS and, thus, appeared to be a new Pm gene. Examination of the genotype frequencies in the F2:3 families showed that a genetic variation in the PmWE99 interval that favored the transmission of the WE99 allele could be the cause of the deviated segregation. Further investigation revealed that the abnormal segregation only occurred at the PmWE99 interval and was not common at other loci in this population. Identification of PmWE99 will increase the diversity of the Pm genes for wheat improvement.

Pollen Killer Gene S35 Function Requires Interaction with an Activator That Maps Close to S24, Another Pollen Killer Gene in Rice.

Pollen killer genes disable noncarrier pollens, and are responsible for male sterility and segregation distortion in hybrid populations of distantly related plant species. The genetic networks and the molecular mechanisms underlying the pollen killer system remain largely unknown. Two pollen killer genes, S24 and S35, have been found in an intersubspecific cross of Oryza sativa ssp. indica and japonica. The effect of S24 is counteracted by an unlinked locus EFS. Additionally, S35 has been proposed to interact with S24 to induce pollen sterility. These genetic interactions are suggestive of a single S24-centric genetic pathway (EFS–S24–S35) for the pollen killer system. To examine this hypothetical genetic pathway, the S35 and the S24 regions were further characterized and genetically dissected in this study. Our results indicated that S35 causes pollen sterility independently of both the EFS and S24 genes, but is dependent on a novel gene close to the S24 locus, named incentive for killing pollen (INK). We confirmed the phenotypic effect of the INK gene separately from the S24 gene, and identified the INK locus within an interval of less than 0.6 Mb on rice chromosome 5. This study characterized the genetic effect of the two independent genetic pathways of INK–S35 and EFS–S24 in indica–japonica hybrid progeny. Our results provide clear evidence that hybrid male sterility in rice is caused by several pollen killer networks with multiple factors positively and negatively regulating pollen killer genes.

Extent and overlap of segregation distortion regions in 12 barley crosses determined via a Pool-GBS approach.

Extent and overlap of segregation distortion regions in 12 barley crosses determined via a Pool-GBS approach. Segregation distortion is undesirable as it alters the frequency of alleles and can reduce the chances of obtaining a particular combination of alleles. In this work, we have used a pooled genotyping-by-sequencing (Pool-GBS) approach to estimate allelic frequencies and used it to examine segregation distortion in 12 segregating populations of barley derived from androgenesis. Thanks to the extensive genome-wide SNP coverage achieved (between 674 and 1744 markers), we determined that the proportion of distorted markers averaged 28.9% while 25.3% of the genetic map fell within segregation distortion regions (SDRs). These SDRs were characterized and identified based on the position of the marker showing the largest distortion and the span of each SDR. Summed across all 12 crosses, 36 different SDR peaks could be distinguished from a total of 50 SDRs and a majority of these SDRs (27 of 36) were observed in only one population. While most shared SDRs were common to only two crosses, two SDRs (SDR3.1 and SDR4.2) were exceptionally recurrent (seen in five and four crosses, respectively). Because of the broad span of most SDRs, an average of 30% of crosses showed segregation distortion in any given chromosomal segment. In reciprocal crosses, although some SDRs were clearly shared, others were unique to a single direction. In summary, segregation distortion is highly variable in its extent and the number of loci underpinning these distortions seems to be quite large even in a narrow germplasm such as six-row spring barley.

High-density linkage mapping and distribution of segregation distortion regions in the oak genome.

We developed the densest single-nucleotide polymorphism (SNP)-based linkage genetic map to date for the genus Quercus. An 8k gene-based SNP array was used to genotype more than 1,000 full-sibs from two intraspecific and two interspecific full-sib families of Quercus petraea and Quercus robur. A high degree of collinearity was observed between the eight parental maps of the two species. A composite map was then established with 4,261 SNP markers spanning 742 cM over the 12 linkage groups (LGs) of the oak genome. Nine genomic regions from six LGs displayed highly significant distortions of segregation. Two main hypotheses concerning the mechanisms underlying segregation distortion are discussed: genetic load vs. reproductive barriers. Our findings suggest a predominance of pre-zygotic to post-zygotic barriers.

Genotyping-by-Sequencing on Pooled Samples and its Use in Measuring Segregation Bias during the Course of Androgenesis in Barley.

Estimation of allelic frequencies is often required in breeding but genotyping many individuals at many loci can be expensive. We have developed a genotyping-by-sequencing (GBS) approach for estimating allelic frequencies on pooled samples (Pool-GBS) and used it to examine segregation distortion in doubled haploid (DH) populations of barley ( L.). In the first phase, we genotyped each line individually and exploited these data to explore a strategy to call single nucleotide polymorphisms (SNPs) on pooled reads. We measured both the number of SNPs called and the variance of the estimated allelic frequencies at various depths of coverage on a subset of reads containing 5 to 25 million reads. We show that allelic frequencies could be cost-effectively and accurately estimated at a depth of 50 reads per SNP using 15 million reads. This Pool-GBS approach yielded 1984 SNPs whose allelic frequency estimates were highly reproducible (CV = 10.4%) and correlated ( = 0.9167) with the "true" frequency derived from analysis of individual lines. In a second phase, we used Pool-GBS to investigate segregation bias throughout androgenesis from microspores to a population of regenerated plants. No strong bias was detected among the microspores resulting from the meiotic divisions, whereas significant biases could be shown to arise during embryo formation and plant regeneration. In summary, this methodology provides an approach to estimate allelic frequencies more efficiently and on materials that are unsuitable for individual analysis. In addition, it allowed us to shed light on the process of androgenesis in barley.

Spinocerebellar ataxia type 3/Machado-Joseph disease: segregation patterns and factors influencing instability of expanded CAG transmissions.

Controversies about Mendelian segregation and CAG expansion (CAGexp) instabilities during meiosis in spinocerebellar ataxia type 3/Machado-Joseph disease (SCA3/MJD) need clarification. Additional evidence about these issues was obtained from the cohort of all SCA3/MJD individuals living in South Brazil. A survey was carried out to update information registered since 2001. Deaths were checked with the Public Information System, and data was made anonymous. Anticipation and delta-CAGexp from parent-offspring pairs, and delta-CAGexp between siblings were obtained. One hundred and fifty-nine families (94% of the entire registry) were retrieved, comprising 3725 living individuals as of 2015, 625 of these being symptomatic. Minimal prevalence was 6:100,000. Carriers of a CAGexp represented 65.6% of sibs in the genotyped offspring (p < 0.001). Median instability was larger among paternal than maternal transmissions, and instabilities correlated with anticipation (r = 0.38; p = 0.001). Age of the parent correlated to delta-CAGexp among 115 direct parent-offspring CAGexp transmissions (ρ = 0.23, p = 0.014). In 98 additional kindreds, the delta-CAGexp between 269 siblings correlated with their delta-of-age (ρ = 0.27, p < 0.0001). SCA3/MJD was associated with a segregation distortion favoring the expanded allele in our cohort. Instability of expansion during meiosis was weakly influenced by the age of the transmitting parent at the time of conception.

Mechanisms of sex determination and transmission ratio distortion in Aedes aegypti.

BackgroundMore effective mosquito control strategies are urgently required due to the increasing prevalence of insecticide resistance. The sterile insect technique (SIT) and the release of insects carrying a dominant lethal allele (RIDL) are two proposed methods for environmentally-friendly, species-targeted population control. These methods may be more suitable for developing countries if producers reduce the cost of rearing insects. The cost of control programs could be reduced by producing all-male mosquito populations to circumvent the isolation of females before release without reducing male mating competitiveness caused by transgenes.ResultsAn RNAi construct targeting the RNA recognition motif of the Aedes aegypti transformer-2 (tra-2) gene does not trigger female-to-male sex conversion as commonly observed among dipterous insects. Instead, homozygous insects show greater mortality among m-chromosome-bearing sperm and mm zygotes, yielding up to 100 % males in the subsequent generations. The performance of transgenic males was not significantly different to wild-type males in narrow-cage competitive mating experiments.ConclusionOur data provide preliminary evidence that the knockdown of Ae. aegypti tra-2 gene expression causes segregation distortion acting at the level of gametic function, which is reinforced by sex-specific zygotic lethality. This finding could promote the development of new synthetic sex distorter systems for the production of genetic sexing mosquito strains.Electronic supplementary materialThe online version of this article (doi:10.1186/s13071-016-1331-x) contains supplementary material, which is available to authorized users.

A highly recombined, high-density, eight-founder wheat MAGIC map reveals extensive segregation distortion and genomic locations of introgression segments.

SummaryMultiparent Advanced Generation Intercross (MAGIC) mapping populations offer unique opportunities and challenges for marker and QTL mapping in crop species. We have constructed the first eight‐parent MAGIC genetic map for wheat, comprising 18 601 SNP markers. We validated the accuracy of our map against the wheat genome sequence and found an improvement in accuracy compared to published genetic maps. Our map shows a notable increase in precision resulting from the three generations of intercrossing required to create the population. This is most pronounced in the pericentromeric regions of the chromosomes. Sixteen percent of mapped markers exhibited segregation distortion (SD) with many occurring in long (>20 cM) blocks. Some of the longest and most distorted blocks were collinear with noncentromeric high‐marker‐density regions of the genome, suggesting they were candidates for introgression fragments introduced into the bread wheat gene pool from other grass species. We investigated two of these linkage blocks in detail and found strong evidence that one on chromosome 4AL, showing SD against the founder Robigus, is an interspecific introgression fragment. The completed map is available from http://www.niab.com/pages/id/326/Resources.

High levels of segregation distortion in the molecular linkage map of bread wheat representing the West Asia and North Africa region

The Fertile Crescent is a primary center of wheat domestication and diversity. Despite its importance for bread wheat breeding, few efforts have been made to fully understand the genetic structure of the Anatolian bread wheat. A lack of information regarding the genetic structure of the bread wheat from this region is evident. Therefore, this study aimed to provide new insights into the genetic structure of bread wheat from Anatolia. A genetic linkage map was constructed based on recombinant inbred lines derived from a cross between the Turkish cultivar Gerek-79 and the Moroccan cultivar Arrehane, by using DArT markers anchored with simple sequence repeat markers. This map consisted of 54 linkage groups belonging to 21 bread wheat chromosomes, spanning a total of 935.629 cM. The total number of mapped markers varied from 5 to 87, depending on the chromosome. Seventy-seven DArT markers with unpublished chromosomal locations were mapped on different chromosomes, whereas 23 were mapped onto chromosomes that deviated from those detailed in the literature. This linkage map represents a key starting point towards our understanding of the genome structure of Anatolian bread wheat, which would, in turn, permit us to genetically dissect important agromorphological and quality characteristics. This linkage map will be useful for the identification of QTL for biotic and abiotic stresses, and for important agronomic traits that are valuable for Anatolian wheat.

Identification and characterization of genic microsatellites in Cunninghamia lanceolata (Lamb.) Hook (Taxodiaceae)

Genomic resources for conventional breeding programs are extremely limited for coniferous trees, and existing simple sequence repeat markers are usually identified through the laborious process of hybridization screening. Therefore, this study aimed to identify gene-based microsatellites in the Chinese fir, Cunninghamia lanceolata (Lamb.) Hook by screening transcript data. We identified 5200 microsatellites. Trinucleotide motifs were most common (47.94%) and were followed by tetranucleotide motifs (24.92%). The AG/CT motif (43.93%) was the most abundant dinucleotide repeat, whereas AAG/CTT (25.07%) was the most common trinucleotide repeat. A total of 411 microsatellite primer pairs were designed and 97 polymorphic loci were identified by 8 genotypes. The number of alleles per locus (Na) in these polymorphic loci ranged from 2 to 5 (mean, 2.640), the Ho values were 0.000-1.000 (mean, 0.479), and the HE values were 0.125-0.775 (mean, 0.462). The polymorphic information content (PIC) values were 0.110-0.715 (mean, 0.383). Seventy-two of the 97 polymorphic markers (74.23%) were present within genes with predicted functions. In addition, in genetic diversity and segregation analyses of 16 genotypes, only 5.88% of the polymorphic loci displayed segregation distortion at the p&lt;0.05 level. Transferable amplification of a randomly selected set of 30 genic microsatellites showed that transferability decreased with increasing evolutionary distance between C. lanceolata and target conifers. Thus, these 97 genic markers will be useful for genetic diversity analysis, germplasm characterization, genome mapping and marker-assisted breeding in C. lanceolata, and evolutionary genetic analysis in Taxodiaceae.

Construction of a Genetic Linkage Map and QTL Analysis of Fruit-related Traits in an F1 Red Fuji x Hongrou Apple Hybrid

AbstractA genetic linkage map of the apple, composed of 175 SSR and 105 SRAP markers, has been constructed using 110 F1 individuals obtained from a cross between the ‘Red Fuji’ Malus domestica and ‘Hongrou’ Malus sieversii cultivars, which have relatively high levels of DNA marker polymorphism and differ remarkably in fruit-related traits. The linkage map comprised 17 linkage groups, covering 1299.67 cM with an average marker distance of 4.6 cM between adjacent markers, or approximately 91% of Malus genome. Linkage groups were well populated and, although marker density ranged from 2.1 to 9.5 cM, just 10 gaps of more than 15 cM were observed. Moreover, just 12.5% of markers displayed segregation distortion. The present genetic linkage map was used to identify quantitative trait loci (QTLs) affecting fruit-related traits. 23 QTLs for ten fruit traits were detected by multiple interval mapping: 3 QTLs for Vc content, One QTL for single fruit weight, 2 QTLs for peel-phenols content, 2 QTLs for flesh-hardness, 2 QTLs for diameter, 6 QTLs for acid content, 1 QTL for sugar content, 2 QTLs for soluble solids content, 2 QTLs for flesh-phenols and 2 QTLs for brittleness. These QTLs were located on linkage groups C1, C2, C3, C5, C6, C7, C9, C10, C14 and C17, respectively. The phenotypic variations exhibited by each QTL ranged from 2% to 72%, and their LOD values varied from 2.03 to 8.93, of which five QTLs were major effect genes (R2 ≥ 10%). The tight linkage markers (*me2em7-460f, *MS01a03-180m, *me1em6-307m, *CH05c06-102f, *me1em8-423f) would be helpful to elucidate the molecular mechanisms of apple domestication and breeding in the future.