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1.
Mittal U Sharma S Chopra R Dheeraj K Pal PK Srivastava AK Mukerji M 《Human genetics》2005,118(1):107-114
There is a wide variation in prevalence of spinocerebellar ataxia type 1 (SCA1) in different populations. In the present study, we observed SCA1 in ∼22% (37/167 families) of the autosomal dominant cerebellar ataxias (ADCAs) in the Indian population. We investigated the role of various genetic factors like repeat length, interruption pattern and chromosomal background in predisposing the repeats to instability in these families. We analyzed 12 markers (9 SNPs and 3 microsatellite markers) and found 3 of them, spanning a region of ∼65 kbp to be linked with the disease locus in the Indian population. The haplotype C-4-C defined by rs1476464 (SNP9)-D6S288-rs2075974 (SNP1), which was extremely rare in nonaffected chromosomes (∼3%), was observed to be significantly (P<0.0000) associated with the expanded chromosomes in ∼44% of SCA1 families. This haplotype was found in all nonhuman primates. SNP1 (C/T), which showed a skewed allelic distribution between large (LN > 30 repeats) and small normal (SN ≤ 30 repeats) alleles (P<0.0000) had similar allelic distribution (P=0.3477) in LN and expanded alleles. Our study suggested that LN and expanded chromosomes linked with the ancestral C allele of SNP1 might have originated simultaneously during evolution by the lengthening of repeats. The LN alleles might have accumulated repeat stabilizing non-CAG interruptions during this process. Similar proportions of T allele in SN with single interruptions, LN and expanded chromosomes lend credence to the origin of expanded alleles from singly-interrupted chromosomes. Our analyses using markers linked (anchoring) to SCA1 suggest that prevalence of SCA1 is correlated to both repeat length and number of interruptions in the Indian population. The spectrum of these alleles also points toward the antiquity of SCA1 mutation in the Indian population.Electronic Supplementary Material Supplementary material is available for this article at 相似文献
2.
Garcés-Claver A Fellman SM Gil-Ortega R Jahn M Arnedo-Andrés MS 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》2007,115(7):907-916
A single nucleotide polymorphism (SNP) associated with pungency was detected within an expressed sequence tag (EST) of 307 bp.
This fragment was identified after expression analysis of the EST clone SB2-66 in placenta tissue of Capsicum fruits. Sequence alignments corresponding to this new fragment allowed us to identify an SNP between pungent and non-pungent
accessions. Two methods were chosen for the development of the SNP marker linked to pungency: tetra-primer amplification refractory
mutation system-PCR (tetra-primer ARMS-PCR) and cleaved amplified polymorphic sequence. Results showed that both methods were
successful in distinguishing genotypes. Nevertheless, tetra-primer ARMS-PCR was chosen for SNP genotyping because it was more
rapid, reliable and less cost-effective. The utility of this SNP marker for pungency was demonstrated by the ability to distinguish
between 29 pungent and non-pungent cultivars of Capsicum annuum. In addition, the SNP was also associated with phenotypic pungent character in the tested genotypes of C. chinense, C. baccatum, C. frutescens, C. galapagoense, C. eximium, C. tovarii and C. cardenasi. This SNP marker is a faster, cheaper and more reproducible method for identifying pungent peppers than other techniques
such as panel tasting, and allows rapid screening of the trait in early growth stages. 相似文献
3.
该研究利用筛选出的7对SSR引物,对中国20个省、市、自治区的210份种质资源进行分子标记试验,分析中国黄连木种质资源遗传多样性、亲缘关系、遗传分化特点并构建DNA分子身份证,为黄连木的资源保护、种质利用提供理论依据,结果表明:(1)7对引物在210份种质中共扩增出158个等位基因位点,平均每对引物的等位基因数为22.571个。(2)基因多样性(GD)变化幅度为0.654~0.913,平均为0.804;期望杂合度(He)变化范围0.257~0.771,平均为0.532;多态信息含量(PIC)变化范围0.639~0.907,平均为0.784。(3)从不同地区黄连木群体的遗传多样性来看,观测杂合度(Ho)介于0.373~0.600之间,平均值为0.520;期望杂合度(He)介于0.632~0.811之间,平均值为0.737;从各群体间遗传分化指数(Fst)来看,黄连木各地区群体间的遗传分化值在0.015~0.099之间,各群体间的遗传分化处于中等以下水平。(4)分子方差分析(AMOVA)结果显示,黄连木的遗传分化变异以群体内为主,占总变异量的94%,群体间的变异占6%。(5)UPGMA聚类、群体遗传结构分析和PCoA分析结果相一致,全部种质被划分为两大类,西南地区群体单独为一类,其他地区单独为一类。(6)利用7对SSR引物构建了210份黄连木种质的DNA分子身份证。 相似文献
4.
Ran Wang Siyuan Xing Peter M. Bourke Xiuquan Qi Miaomiao Lin Danny Esselink Paul Arens Roeland E. Voorrips Richard G.F. Visser Leiming Sun Yunpeng Zhong Hong Gu Yukuo Li Sikai Li Chris Maliepaard Jinbao Fang 《Plant biotechnology journal》2023,21(2):369-380
Kiwifruit (Actinidia spp) is a woody, perennial and deciduous vine. In this genus, there are multiple ploidy levels but the main cultivated cultivars are polyploid. Despite the availability of many genomic resources in kiwifruit, SNP genotyping is still a challenge given these different levels of polyploidy. Recent advances in SNP array technologies have offered a high-throughput genotyping platform for genome-wide DNA polymorphisms. In this study, we developed a high-density SNP genotyping array to facilitate genetic studies and breeding applications in kiwifruit. SNP discovery was performed by genome-wide DNA sequencing of 40 kiwifruit genotypes. The identified SNPs were stringently filtered for sequence quality, predicted conversion performance and distribution over the available Actinidia chinensis genome. A total of 134 729 unique SNPs were put on the array. The array was evaluated by genotyping 400 kiwifruit individuals. We performed a multidimensional scaling analysis to assess the diversity of kiwifruit germplasm, showing that the array was effective to distinguish kiwifruit accessions. Using a tetraploid F1 population, we constructed an integrated linkage map covering 3060.9 cM across 29 linkage groups and performed QTL analysis for the sex locus that has been identified on Linkage Group 3 (LG3) in Actinidia arguta. Finally, our dataset presented evidence of tetrasomic inheritance with partial preferential pairing in A. arguta. In conclusion, we developed and evaluated a 135K SNP genotyping array for kiwifruit. It has the advantage of a comprehensive design that can be an effective tool in genetic studies and breeding applications in this high-value crop. 相似文献
5.
Correlation Between Pneumocystis jirovecii Mitochondrial Genotypes and High and Low Fungal Loads Assessed by Single Nucleotide Primer Extension Assay and Quantitative Real‐Time PCR
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Alexandre Alanio Martine Olivi Odile Cabaret Françoise Foulet Anne‐Pauline Bellanger Laurence Millon Ana Berceanu Catherine Cordonnier Jean‐Marc Costa Stéphane Bretagne 《The Journal of eukaryotic microbiology》2015,62(5):650-656
We designed a single nucleotide primer extension (SNaPshot) assay for Pneumocystis jirovecii genotyping, targeting mt85 SNP of the mitochondrial large subunit ribosomal RNA locus, to improve minority allele detection. We then analyzed 133 consecutive bronchoalveolar lavage (BAL) fluids tested positive for P. jirovecii DNA by quantitative real‐time PCR, obtained from two hospitals in different locations (Hospital 1 [n = 95] and Hospital 2 [n = 38]). We detected three different alleles, either singly (mt85C: 39.1%; mt85T: 24.1%; mt85A: 9.8%) or together (27%), and an association between P. jirovecii mt85 genotype and the patient's place of hospitalization (p = 0.011). The lowest fungal loads (median = 0.82 × 103 copies/μl; range: 15–11 × 103) were associated with mt85A and the highest (median = 1.4 × 106 copies/μl; range: 17 × 103–1.3 × 107) with mt85CTA (p = 0.010). The ratios of the various alleles differed between the 36 mixed‐genotype samples. In tests of serial BALs (median: 20 d; range 4–525) from six patients with mixed genotypes, allele ratio changes were observed five times and genotype replacement once. Therefore, allele ratio changes seem more frequent than genotype replacement when using a SNaPshot assay more sensitive for detecting minority alleles than Sanger sequencing. Moreover, because microscopy detects only high fungal loads, the selection of microscopy‐positive samples may miss genotypes associated with low loads. 相似文献
6.
The overlapping ranges of closely related species provide a natural setting for the investigation of reticulate hybridization
and other evolutionary processes. In the present study, we examined the pattern of genetic variation and interspecific gene
flow in seven Actinidia species across ten localities in which sympatry among at least two species occurs. Our results showed that 48.7% of the alleles
across the nine nuclear microsatellite loci examined were shared among the seven Actinidia species. Moreover, at the species level, Actinidia chinensis and Actinidia deliciosa exhibited the highest genetic similarity, with a large percentage of shared alleles (P
s = 81.3%) and a significant consistency between the distribution frequency of their allele sizes (r = 0.859, P = 0.045). Yet, the genetic distinctions between species are obvious except for the species pair A. chinensis and A. deliciosa. Interspecific introgression was detected among the two main species pairs (Actinidia latifolia–Actinidia eriantha and A. chinensis–A. deliciosa), but more apparent in the latter in which 30% of the A. chinensis individuals and 49% of the A. deliciosa individuals showed genetic admixture in the STRUCTURE analysis. Possibly active hybrid zones relating to the two main species
pairs were discussed at last, which are expected to pave the way for the introgression breeding of kiwifruit from natural
sympatric populations. 相似文献
7.
Oliver Treeck Esma Elemenler Christina Kriener Felicitas Horn Anette Springwald Arndt Hartmann Olaf Ortmann 《The Journal of steroid biochemistry and molecular biology》2009,114(3-5):207-211
Genetic variations like single nucleotide polymorphisms (SNPs) in genes involved in estrogen biosynthesis, metabolism and signal transduction have been suggested to affect breast cancer susceptibility. In this study we tested the hypothesis that polymorphisms in the promoter of ESR2 gene may be associated with increased risk for breast cancer. We analyzed three SNPs in the promoter region of human ESR2 gene by means of allele-specific tetra-primer PCR. A total of 318 sporadic breast cancer cases and 318 age-matched controls were included in the study. With regard to homozygous genotypes, women with sporadic breast cancer more frequently carried the CC genotype of ESR2 promoter SNP rs2987983 (OR 1.99, p = 0.005). Calculation of allele positivity demonstrated that presence of T allele of this SNP was more frequent in healthy women. Our data suggest that a SNP in the promoter region of ESR2 gene might be able to affect breast cancer risk. These results further support the emerging hypothesis that ERβ is an important factor in breast cancer development. 相似文献
8.
We report on the isolation and characterization of eight microsatellite markers from repetitive DNA enriched libraries for
Cryptocarya chinensis from lower subtropical China. These are the first microsatellite loci reported for Cryptocarya species. The number of alleles ranged from three to nine. Observed and expected heterozygosities ranged from 0.0518 to 0.9910
and 0.5241 to 0.7935 for polymorphic loci, respectively. These markers will allow analyses of the baseline genetic variability
and population structure of C. chinensis to enrich our scientific understanding of forest fragmentation on genetic health of this species and provide strategies for
effective conservation and management in this area. 相似文献
9.
In this study, the genotype distribution and allelic frequencies of CAPN1 (Calcium activated neutral protease) single nucleotide polymorphisms (SNPs) were analyzed taking advantage of the different
genetic backgrounds provided by Hereford, Brahman and Braford cattle. We report a new insertion/deletion (InDel) polymorphism,
consisting of a change of seven nucleotides for only one nucleotide (TCTGGGT → C) within intron 17 of the CAPN1 gene. The segregation pattern of this polymorphism was analyzed together with the markers CAPN316, CAPN530 and CAPN4751 already
described. The allele distribution of CAPN1 markers in the Braford crossbreed (3/8 Brahman 5/8 Hereford) is described for the first time. Four assays of allelic discrimination
were designed: the tetra primer ARMS-PCR technique for genotyping the new InDel and the CAPN4751 marker, and a PCR-RFLP method
for genotyping the markers CAPN316 and CAPN530. The genotypic and minor allele frequencies (MAFs) obtained showed that the
InDel polymorphism does not provide redundant information to that already provided by the other CAPN1 markers and segregates differently between breeds, being a common SNP (MAF ≥ 0.05) in the herds with a high percentage of
Bos indicus background. The high percentage of heterozygous individuals found in the Braford crossbreed for the markers assessed reveals
enough genetic variation that could help to solve the tenderness problem of tropical-adapted cattle. 相似文献
10.
The objective of this study was to identify genetic markers and genomic regions associated with susceptibility to Mycobacterium avium ssp. paratuberculosis (MAP) infection in Holstein cattle. Associated single nucleotide polymorphisms (SNPs) were identified by genotyping 521 MAP‐infected Holstein cows and comparing SNP allele frequencies of these infected cows with allele frequencies estimated from specific reference populations. Reference population allele frequency estimates used Holstein sire genotype data and were weighted estimates based on sire usage within the population in question. The 521 infected cows were 233 and 288 cows from two resource populations of approximately 5000 cows each, collected independently. Population 1 was comprised primarily of daughters of twelve Holstein artificial insemination sires used heavily within the US dairy cattle population. Samples were obtained from 300 co‐operating commercial dairy herds throughout the US and were tested by both MAP faecal culture and blood‐enzyme‐linked immunosorbent assay (ELISA). Population 2 consisted of dairy cattle from six co‐operating dairy herds in Wisconsin, with all animals in the herds tested by blood enzyme‐linked immunosorbent assay (ELISA) for MAP infection. Genotyping was performed with the Illumina Bovine SNP50 Bead Chip, providing genotypes for 35 772 informative SNPs. Data from the two resource populations were analysed both in separate and combined analyses. The most significant autosomal markers from the individual and combined analyses (n = 197, nominal P < 0.001) were used in a stepwise logistic regression analysis to identify a set of 51 SNPs that could be used as a predictor of genetics for Holstein cattle susceptibility to MAP infection. 相似文献
11.
W. L. Bai C. Y. Zhou Y. Ren R. H. Yin W. Q. Jiang S. J. Zhao S. C. Zhang B. L. Zhang G. B. Luo Z. H. Zhao 《Molecular biology reports》2011,38(1):471-479
The aim of the present work was to investigate single nucleotide polymorphism (SNP) of growth hormone receptor (GHR) gene exon 10, characterize the genetic variation in three Chinese indigenous goat breeds, and search for its potential association
with cashmere traits. In this study, a polymerase chain reaction-single strand conformation polymorphism (PCR–SSCP) protocol
has been developed for rapid genotyping of the GHR gene in goats. One hundred seventy-eight goats from Liaoning Cashmere (96), Inner Mongolia White Cashmere (40), and Chengdu
Grey (42) breeds in China were genotyped at GHR locus using the protocol developed. In all goat breeds investigated, a SNP in exon 10 of GHR gene has been identified by analyzing genomic DNA. The polymorphism consists of a single nucleotide substitution A → G, resulting
in two alleles named, respectively, A and G based on the nucleotide at the position. The allele A was found to be more common
in the animals investigated, and seems to be more consistent with cattle and zebu at this polymorphic site found in goats.
The Hardy–Weinberg equilibrium of genotype distributions of GHR locus was verified in Liaoning Cashmere, and Inner Mongolia White Cashmere breeds. According to the classification of polymorphism
information content (PIC), Chengdu Grey was less polymorphic than Liaoning Cashmere and Inner Mongolia White Cashmere breeds at this locus. The phylogenetic
tree of different species based on the nucleotide sequences of GHR gene exon 10 is generally in agreement with the known species relationship. No significant association was found between
the polymorphism revealed and the cashmere traits analyzed in present work. 相似文献
12.
Qiang Fan Sufang Chen Renchao Zhou Xu Xiang Wenbo Liao Suhua Shi 《Conservation Genetics》2011,12(3):753-760
Understanding the amount and distribution of genetic diversity in natural populations can inform the conservation strategy
for the species in question. In this study, genetic variation at eight nuclear microsatellite loci was used to investigate
genetic diversity and population structure of wild litchi (Litchi chinensis Sonn. subsp. chinensis). Totally 215 individuals were sampled, representing nine populations of wild litchi. All eight loci were polymorphic, with
a total of 51 alleles. The expected heterozygosity in the nine populations ranged from 0.367 to 0.638 with an average value
of 0.526. Inbreeding within wild litchi populations was indicated by a strong heterozygote defect. Significant bottleneck
events were detected in the populations from Yunnan and Vietnam, which could be responsible for lower levels of genetic diversity
in these populations. Measures of genetic differentiation (F
ST = 0.269) indicated strong differentiation among wild litchi populations. Significant correlation was found between genetic
differentiation and geographical distance (r = 0.655, P = 0.002), indicating a strong isolation by distance in these populations. Bayesian clustering suggested genetic separation
among three regional groups, namely, the western group, the central group and the eastern group. Some conservation strategies
for wild litchi populations were also proposed based on our results. 相似文献
13.
Xiuli Wang Xiaoli Guo Yingming Zhang Xiangying Meng Xuemei Qiu Shaozhen Liu Tianxiao Zhang 《Conservation Genetics》2009,10(5):1455-1457
In our study, we evaluated simple sequence repeat (SSR) markers from expressed sequence tags (ESTs) of Fenneropenaeus chinensis. Characteristics of 11 EST-SSR loci were investigated using 34 F. chinensis individuals. The number of alleles per locus ranged from 4 to 9. The observed heterozygosity ranged from 0.118 to 0.826,
while the expected heterozygosity ranged from 0.623 to 0.847. Two loci (T2 and T12) conformed to the Hardy–Weinberg equilibrium.
There was no LD observed between all pairs of EST-SSRs loci. The PIC values of 11 microsatellite loci were higher than 0.5.
These loci and markers will be useful for population genetics and systemic evolution of F. chinensis. 相似文献
14.
Peter Westermeier Gerhard Wenzel Volker Mohler 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》2009,119(7):1301-1311
Single-nucleotide polymorphisms (SNPs) and insertion–deletions (INDELs) are currently the important classes of genetic markers
for major crop species. In this study, methods for developing SNP markers in rapeseed (Brassica napus L.) and their in silico mapping and use for genotyping are demonstrated. For the development of SNP and INDEL markers, 181
fragments from 121 different gene sequences spanning 86 kb were examined. A combination of different selection methods (genome-specific
amplification, hetero-duplex analysis and sequence analysis) allowed the detection of 18 singular fragments that showed a
total of 87 SNPs and 6 INDELs between 6 different rapeseed varieties. The average frequency of sequence polymorphism was estimated
to be one SNP every 247 bp and one INDEL every 3,583 bp. Most SNPs and INDELs were found in non-coding regions. Polymorphism
information content values for SNP markers ranged between 0.02 and 0.50 in a set of 86 varieties. Using comparative genetics
data for B. napus and Arabidopsis thaliana, an allocation of SNP markers to linkage groups in rapeseed was achieved: a unique location was determined for seven gene
sequences; two and three possible locations were found for six and four sequences, respectively. The results demonstrate the
usefulness of existing genomic resources for SNP discovery in rapeseed. 相似文献
15.
Luca Fontanesi Francesca Bertolini Stefania Dall'Olio Luca Buttazzoni Maurizio Gallo Vincenzo Russo 《Animal biotechnology》2013,24(3):147-155
In pigs, susceptibility to enterotoxigenic Escherichia coli (ETEC) K88 strains (locus F4bcR) is determined by a dominant allele, with the recessive allele determining resistance. The susceptible allele also appeared to be associated with higher growth rate even with discordant results. A single nucleotide polymorphism (SNP) in exon 7 of the mucin 4 (MUC4) gene (DQ848681:g.8227C>G), shown to be in close linkage disequilibrium with the F4bcR locus, has been used as marker to identify susceptible pigs, substituting invasive villous adhesion tests. We herein analyzed this SNP in Italian local breeds and applied a selective genotyping approach in Italian Large White, Italian Landrace, and Italian Duroc comparing allele frequency distribution in groups of pigs with extreme estimated breeding values (EBV) for average daily gain (ADG) and backfat thickness (BFT) to evaluate if this marker is associated with these traits. Allele G (associated with susceptibility to ETEC) was associated with higher ADG and BFT in Italian Large White (P = 6.66E-04 and P = 0.012, respectively) and higher ADG in Italian Landrace (P = 7.23E-12). This polymorphism was poorly informative in Italian Duroc. Antagonistic associations of the MUC4 g.8227C>G alleles on susceptibility to ETEC and growth performances evidence the complexity of applying marker assisted selection in pig breeding. 相似文献
16.
Analysis of single nucleotide polymorphisms (SNPs) has been and will be increasingly utilized in various genetic disciplines, particularly in studying genetic determinants of complex diseases. Such studies will be facilitated by rapid, simple, low cost and high throughput methodologies for SNP genotyping. One such method is reported here, named tetra-primer ARMS-PCR, which employs two primer pairs to amplify, respectively, the two different alleles of a SNP in a single PCR reaction. A computer program for designing primers was developed. Tetra-primer ARMS-PCR was combined with microplate array diagonal gel electrophoresis, gaining the advantage of high throughput for gel-based resolution of tetra-primer ARMS-PCR products. The technique was applied to analyse a number of SNPs and the results were completely consistent with those from an independent method, restriction fragment length polymorphism analysis. 相似文献
17.
Seven polymorphic and transferable nuclear microsatellites were used to investigate the population structure of genetic diversity
of Schisandra chinensis and Schisandra sphenanthera for facilitating their conservation and sustainable utilization. High levels of gene diversity were revealed in these two
medicinal species, the majority of genetic diversity was harbored within populations, and population structure was might due
to restricted gene flow among populations. Isolation by distance was close to significance in S. chinensis but not in S. sphenanthera. In S. chinensis, null alleles were identified as a cause for excess of homozygotes at loci G24 and WGA60, but inbreeding might also be partly
responsible for the positive F
IS
values in this species. In contrast, null allele frequencies were high at all the seven loci in S. sphenanthera and resulted in overestimation of fixation index. The strategy for ex situ conservation of these two medicinal species is
discussed based on the genetic results. 相似文献
18.
Neele Wendler Martin Mascher Christiane Nöh Axel Himmelbach Uwe Scholz Brigitte Ruge‐Wehling Nils Stein 《Plant biotechnology journal》2014,12(8):1122-1131
Crop wild relatives (CWR) provide an important source of allelic diversity for any given crop plant species for counteracting the erosion of genetic diversity caused by domestication and elite breeding bottlenecks. Hordeum bulbosum L. is representing the secondary gene pool of the genus Hordeum. It has been used as a source of genetic introgressions for improving elite barley germplasm (Hordeum vulgare L.). However, genetic introgressions from H. bulbosum have yet not been broadly applied, due to a lack of suitable molecular tools for locating, characterizing, and decreasing by recombination and marker‐assisted backcrossing the size of introgressed segments. We applied next‐generation sequencing (NGS) based strategies for unlocking genetic diversity of three diploid introgression lines of cultivated barley containing chromosomal segments of its close relative H. bulbosum. Firstly, exome capture‐based (re)‐sequencing revealed large numbers of single nucleotide polymorphisms (SNPs) enabling the precise allocation of H. bulbosum introgressions. This SNP resource was further exploited by designing a custom multiplex SNP genotyping assay. Secondly, two‐enzyme‐based genotyping‐by‐sequencing (GBS) was employed to allocate the introgressed H. bulbosum segments and to genotype a mapping population. Both methods provided fast and reliable detection and mapping of the introgressed segments and enabled the identification of recombinant plants. Thus, the utilization of H. bulbosum as a resource of natural genetic diversity in barley crop improvement will be greatly facilitated by these tools in the future. 相似文献
19.
Diego Micheletti Michela Troggio Andrey Zharkikh Fabrizio Costa Mickael Malnoy Riccardo Velasco Silvio Salvi 《Tree Genetics & Genomes》2011,7(4):857-868
Knowledge about the sequence-based genetic diversity of a crop species is important in order to develop highly informative
genotyping assays, which will eventually positively impact breeding practice. Diversity data were obtained from two pools
of 185 and 75 accessions each, representing most of the species belonging to the genus Malus, by re-sequencing 27 gene-specific amplicons and by screening 237 Malus × domestica SNPs using the multiplex genotyping technology SNPlex™. Nucleotide diversity and insertion/deletion rates in M. × domestica were estimated as π = 0.0037 and 1/333 bp, respectively. The SNP frequency was estimated as 0.0194 (1 SNP/52 bp) while within a single apple
cultivar an average of one SNP in every 455 bp was found. We also investigated transferability (T
SNP) of the heterozygous state of SNPs across the species M. × domestica and the genus Malus. Raw re-sequencing showed that 12–15% of M. × domestica SNPs are transferable to a second M. × domestica cultivar, however T
SNP rose to ∼41% with SNPs selected for high minor allele frequency. T
SNP of chosen SNPs averaged ∼27% in the two M. × domestica-related species, Malus sieversii and Malus sylvestris, but was much lower in more distantly related species. On the basis of T
SNP, simulations, and empirical results, we calculated that a close-design, multiplexed genotyping array with at least 2,000
SNPs is required for building a highly saturated linkage maps within any M. × domestica cross. The same array would gradually lose informativeness in increasingly phylogenetically distant Malus species. 相似文献