Relative Genetic Distances Research Articles

Extension of the geographical range of the primary burrowing crayfish Cambarus strigosus Hobbs, 1981 (Decapoda: Astacidea: Cambaridae) in South Carolina

Abstract Knowledge of the geographical distribution for many primary burrowing crayfishes is often limited to information presented in species descriptions or field notes associated with epigean crayfish surveys. Cambarus strigosusHobbs, 1981, a rare primary burrowing crayfish, was collected as part of a survey of the Sumter National Forest, South Carolina (SC), USA. Prior to this discovery, C. strigosus appeared to be endemic to mid-reaches of the Broad River Drainage in Georgia (GA). We conducted additional field sampling in SC and GA and used mitochondrial DNA (mtDNA) to compare the relative genetic distance between individuals across all populations in an effort to determine the identity of the specimens collected. Genetic data indicated that the crayfish collected in SC was C. strigosus, with one shared haplotype between SC and GA populations. Our genetic results exhibited geographic structuring and indicated that SC populations have a specific haplotype unique to them, providing strong evidence that SC populations are not introduced. Two additional SC records of C. strigosus from 1983 housed in the US National Museum were examined and determined to be C. strigosus. With these records, we hypothesized that like in GA, the distribution of C. strigosus in SC is limited to riparian habitats associated with the Savannah River Drainage. While the range of this species has been extended, it is still limited to small portions of this drainage. Thus, further sampling to determine the true extent of C. strigosus distribution within SC along with conservation efforts are needed to protect this globally rare species.

Genetic Map Construction Using F2 and RIL/DH Mapping Population.

Genetic mapping is the determination of the position and relative genetic distance between genes or molecular markers in the chromosomes of a particular species. The construction of genetic maps uses data from the genotyping of the mapping population. Among the different mapping populations used, two are relatively common: the F2 and recombinant inbred lines (RILs) obtained as a result of the controlled crossing of genetically diverse parental forms (e.g., inbred lines). Also, the dihaploid (DH) population is often used in plants, but obtaining DHs in different crops, including rye, is very difficult or even impossible. Any molecular marker system can be used for genotyping. Polymorphic markers are used for linkage analysis, differentiating parental forms with segregation in the mapping population, consistent with the appropriate single-gene model. A genetic map is a great source of information on a species and can be an exquisite tool for analyzing important quantitative traits (QT).This chapter presents the procedure of genetic map construction with two different algorithms using the JoinMap5.0 program. First, the Materials section briefly informs about the mapping program, showing how to obtain a mapping population and prepare data for mapping. Finally, the Methods section describes the protocol for the mapping procedure itself.

Genetic Analysis Reveals Relationships Among Populations of Puccinia striiformis f. sp. tritici from Shaanxi-Gansu-Ningxia-Xinjiang of Northwestern and Sichuan-Yunnan of Southwestern China.

Wheat stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), is one of the most destructive diseases worldwide. In China, wheat stripe rust generally occurs in the northwestern and southwestern regions; however, the genetic relationships of Pst populations between these regions are largely unclear. To determine the population structure and potential migration route in these regions, 235 isolates collected from Xinjiang (XJ), Gansu (GS), Ningxia (NX), Shaanxi (SX), Sichuan (SC), and Yunnan (YN) provinces in 2021 and 2022 were phenotyped using two sets of Pst differentials and genotyped using 20 competitive allele-specific PCR-single nucleotide polymorphism (KASP-SNP) markers. The phenotype tests indicated that CYR34, CYR32, and CYR33 were the predominant races with different occurrence frequencies in different regions and years. Genotypic analysis revealed that a total of 183 multilocus genotypes were identified, and the genetic diversity in the YN subpopulation was the highest. The genetic background in the SX subpopulation was similar to that in the GS and NX subpopulations, and the genetic background in the YN subpopulation was similar to that in the SC and SX subpopulations. A high level of gene flow (Nm) was found between the SX and GS, SX and NX, GS and NX, and SC and YN subpopulations, suggesting the migration of Pst among these regions, while a small amount of Nm existed between the SX and SC subpopulations. SC may serve as a bridge connecting Pst subpopulations between the northwestern provinces (SX, GS, and NX) and the southwestern provinces (SC and YN). With a relatively high genetic distance and low Nm values compared with other Pst subpopulations, XJ is considered a relatively independent epidemiological region in China. These results improved our current understanding of the wheat stripe rust epidemic in northwestern and southwestern regions of China.

Genetic diversity and molecular variability of ’Candidatus Phytoplasma solani’ based on multilocus sequence typing analysis in tomato plantations of western Turkey

‘Candidatus Phytoplasma solani’ (CaPsol) is a very common pathogen in the Euro-Mediterranean regions and has been reported in many countries. Field surveys were conducted in tomato plantations in 2022 to determine the CaPsol infections in the western part of Turkey, which has the highest vegetable production volume. A total of 67 tomato samples, 52 symptomatic and 15 asymptomatic, were collected from four different provinces. A total of thirteen CaPsol strains were identified using molecular techniques from tomato samples. The tuf/stamp/vmp1 genes molecular markers were used to perform molecular and genetic diversity characterizations of these strains. The tuf-b1 genotype and five different stamp genotypes genetically closely related to Eastern European strains were determined in all strains. In addition, these strains showed more than 99% nucleotide sequence similarity with 4 different vmp1 genotypes: V2-TA, V14, V4, and V15. Advanced bioinformatics analyses were performed with stamp (N = 290) and vmp1 (N = 207) strains obtained from this study and GenBank. These analyses showed that the strains for both gene regions descended from two molecular evolutionary ancestors. In order to calculate the genetic distance relationships according to the stamp and vmp1 gene regions, a hierarchical classification was done as geographical and host populations. While these analyses demonstrate the close genetic relationship between Turkish and Eastern European populations, they strongly confirm the importance of the epidemiological cycle between weed, perennial, and insect vectors. Then, molecular variance analyses (AMOVA) were performed on these classified populations. The results indicated high variation for both gene regions but showed that each strain contributed greatly to the CaPsol genetic diversity. Thus, for the first time, multilocus sequence patterns of CaPsol strains obtained from western Turkey were extracted. Extensive genetic analyses have strongly demonstrated the importance of horizontal transmission in the control and epidemiological cycle of CaPsol.

Comparative mitochondrial genomics and phylogenetics for species of the snakehead genus Channa Scopoli, 1777 (Perciformes: Channidae)

The family Channidae, members of which are commonly known as snakehead fish, includes 53 Channa species and three Parachanna species. In this study, we characterized mitochondrial genomes (mitogenomes) of five Channa species (C. andrao, C. bleheri, C. ornatipinnis, C. pulchra, and C. stewartii) for the first time. We compared the mitogenomes with the mitogenomes of 11 other Channidae fish. The newly sequenced mitogenomes were 16,714 – 16,895 bp in length and contained 37 typical genes [13 protein-coding genes (PCGs), two ribosomal RNA genes (rRNAs) and 22 transfer RNA genes (tRNAs)]. Positive AT-skews and negative GC-skews were found in the mitogenomes of Channidae. Most PCGs started with the conventional start codon, ATN; however, the sequence of the stop codon was variable. There was no essential difference in relative synonymous codon usage (RSCU) among the Channidae mitogenomes. The fastest-evolving gene atp8 and slowest-evolving gene cox1 were identified using Ka/Ks and pairwise relative genetic distance (p-distance). The displacement loop (D-loop) regions showed great variability, which affected the size of Channa mitogenomes. One origin of replication on the light strand (OL) region was found between trnN and trnC in the mitogenomes of Channidae. Phylogenetic analysis revealed three new sister pairs (C. andrao + C. bleheri, C. ornatipinnis + C. pulchra, and C. stewartii + C. gachua). Phylogenetic relationships established between the five Channa species based on mitogenomes were also supported by their morphological characteristics and geographical distribution. The novel information we obtained about these mitogenomes will contribute to elucidating the complex relationships among Channa species.

Visualizing Population Structures by Multidimensional Scaling of Smoothed PCA-Transformed Data

Population structure can be revealed using Single Nucleotide Polymorphisms (SNPs) which are genetic variations found in the DNA sequences of individuals. Due to the large number of SNPs, visualization of SNP data is often achieved through dimensionality reduction. Although Principal Component Analysis (PCA) has been extensively used for SNP data visualization, some other dimensionality reduction methods have been shown to be more successful in revealing complex population structures. Nevertheless, these techniques often suffer from reduced ability to preserve the global structure in the SNP data, namely the relative genetic distance between subpopulations, or from high computational cost. In this work, a method which uses Multidimensional Scaling (MDS) of smoothed PCA-transformed data (MSSPD) is proposed. MSSPD successfully reveals population structures in 2D maps, while being more effective than other techniques in preserving the global structure. In terms of computational efficiency, MSSPD is comparable to the fastest SNP visualization methods.

Genetic Diversity and Structure in a Closed Breeding System of Russian Honey Bees.

High levels of genetic diversity are critical to the success of breeding programs. Russian honey bees are a selected stock that undergoes breeding in a closed block-based mating system. Given its established history, Russian stock has longitudinal measures of genetic integrity (i.e., genetically based stock identity) and diversity. Assessments using genetic stock identification (GSI) have shown that genetic diversity parameters were assessed across breeding blocks for three generations, spanning 6 yr (2014, 2017, and 2020), showing levels comparable to those when the stock was initially released in 2008. Allelic richness (mean number of alleles) and gene diversity levels were consistent over time and among blocks. Blocks were generally not differentiated from one another within each year. However, the 2020 population was distinct when compared with bees sampled in both 2014 and 2017. Genetic distance relationships supported differentiation of the 2020 population by distinct clustering. The patterns observed here are consistent with historical changes made to the breeding program to increase stringency of the selection criteria.

Exploring the genetic diversity and population structure of scarlet eggplant germplasm from Rwanda through iPBS-retrotransposon markers.

Scarlet eggplant (Solanum aethiopicum gr. gilo) is a part of African indigenous vegetables and acknowledged as a source of variations in the breeding of Brinjal. Since its genetic diversity is still largely unexplored, therefore genetic diversity and population structure of this plant were investigated in this study. Scarlet eggplant germplasm made of fifty-two accessions originated from two districts of Rwanda was assessed by employing the iPBS-retrotransposon markers system. Twelve most polymorphic primers were employed for molecular characterization and they yielded 329 total bands whereupon 85.03% were polymorphic. The recorded mean polymorphism information content was 0.363 and other diversity indices such as; mean the effective number of alleles, mean Shannon's information index and gene diversity with the following values; 1.298, 0.300 and 0.187 respectively. A superior level of diversity was noticed among accessions from Musanze district. The model-based structure, neighbor-joining, and principal coordinate analysis (PCoA) gathered scarlet germplasm in a divergence manner to their collection district. Analysis of molecular variance (AMOVA) displayed that the utmost variations (81%) in scarlet eggplant germplasm are resulting in differences within populations. The extensive diversity of scarlet eggplant in Rwanda might be used to form the base and genetic resource of an exhaustive breeding program of this economically important African indigenous vegetable. For instance, accessions MZE53 and GKE11 might be proposed as parent candidates due to their high relative genetic distance (0.6781).

A major QTL co-localized on chromosome 6BL and its epistatic interaction for enhanced wheat stripe rust resistance.

Co-localization of a major QTL for wheat stripe rust resistance to a 3.9-cM interval on chromosome 6BL across both populations and another QTL on chromosome 2B with epistatic interaction. Cultivars with diverse resistance are the optimal strategy to minimize yield losses caused by wheat stripe rust (Puccinia striiformis f. sp. tritici). Two wheat populations involving resistant wheat lines P10078 and Snb"S" from CIMMYT were evaluated for stripe rust response in multiple environments. Pool analysis by Wheat660K SNP array showed that the overlapping interval on chromosome 6B likely harbored a major QTL between two populations. Then, linkage maps were constructed using KASP markers, and a co-localized locus with large effect on chromosome 6BL was detected using QTL analysis in both populations. The coincident QTL, named QYr.nwafu-6BL.2, explained 59.7% of the phenotypic maximum variation in the Mingxian 169 × P10078 and 52.5% in the Zhengmai 9023 × Snb"S" populations, respectively. This co-localization interval spanning 3.9cM corresponds to ~ 30.5-Mb genomic region of the newest common wheat reference genome (IWGSC RefSeq v.1.0). In addition, another QTL was also detected on chromosome 2B in Zhengmai 9023 × Snb"S" population and it can accelerate expression of QYr.nwafu-6BL.2 to enhance resistance with epistatic interaction. Allowing for Pst response, marker genotypes, pedigree analysis and relative genetic distance, QYr.nwafu-6BL.2 is likely to be a distinct adult plant resistance QTL. Haplotype analysis of QYr.nwafu-6BL.2 revealed specific SNPs or alleles in the target region from a diversity panel of 176 unrelated wheat accessions. This QTL region provides opportunity for further map-based cloning, and haplotypes analysis enables pyramiding favorable alleles into commercial cultivars by marker-assisted selection.

Relationship of Parental Genetic Distance with Heterosis and Specific Combining Ability in Sesame (Sesamum indicum L.) Based on Phenotypic and Molecular Marker Analysis.

The genetic distance analysis for selection of suitable parents has been established and effectively used in many crops; however, there is dearth of conclusive report of relationship of genetic distance analysis with heterosis in sesame. In the present study, an attempt was made to estimate the associations of genetic distances using SSR (GDSSR), seed-storage protein profiling (GDSDS) and agro-morphological traits (GDMOR) with hybrid performance. Seven parents were selected from 60 exotic and Indian genotypes based on genetic distance from clustering pattern based on SSR, seed-storage protein, morphological traits and per se performance. For combining ability analysis, 7 parents and 21 crosses generated from 7×7 half diallel evaluated at two environments in a replicated field trial during pre-kharif season of 2013. Compared with the average parents yield (12.57gplant-1), eight hybrids had a significant (P<0.01) yield advantage across environments, with averages of 26.94 and 29.99% for better-parent heterosis (BPH) and mid-parent heterosis (MPH), respectively, across environments. Highly significant positive correlation was observed between specific combining ability (SCA) and per se performance (0.97), while positive non-significant correlation of BPH with GDSSR (0.048), and non-significant negative correlations with GDMOR (-0.01) and GDSDS (-0.256) were observed. The linear regressions of SCA on MPH, BPH and per se performance of F1s were significant with R2 value of 0.88, 0.84 and 0.95 respectively. The present findings revealed a weak association of GDSSR with F1's performance; however, SCA has appeared as an important factor in the determination of heterosis and per se performance of the hybrids. The present findings also indicated that parental divergence in the intermediate group would likely produce high heterotic crosses in sesame.

GENETIC DIVERSITY OF CROCUS SATIVUS AND ITS CLOSE RELATIVE SPECIES ANALYZED BY iPBS-RETROTRANSPOSONS

Saffron (Crocus L.) is a member of Crocoideae, the biggest of four subfamilies in the Iridaceae family. It has 2n = 3x = 24 chromosomes and is triploid; thus, it is sterile. In previous research, different molecular DNA markers were used but molecular characterization and genetic diversity of this complex genus have not yet been clarified. Therefore, current study aimed to determine the molecular characterization of saffron and its close relative species using inter-primer binding site (iPBS)-retrotransposon markers. Eighty-three iPBS-retrotransposon primers were used in 28 C. sativus genotypes and 17 close relative species of saffron to identify their genetic diversity. Sixteen polymorphic iPBS-retrotransposon primers generated a total of 401 polymorphic scorable bands. The mean PIC value, Nei’s genetic diversity and Shannon’s information index (I) were calculated as 0.85, 0.16 and 0.29, respectively. The results of the Unweighted Pair Group Method with Arithmetic mean UPGMA dendrogram and Principal Coordinates Analysis PCoA analysis indicated a spatial representation of the relative genetic distances among 28 saffron samples and the 17 close relative species were categorized under two distinct groups. Saffron genotypes showed very limited genetic variation and according to the iPBS-retrotransposon data, its close relatives were C. cartwrightianus and C. pallasii subsp. pallasii.

Rapid identification of an adult plant stripe rust resistance gene in hexaploid wheat by high-throughput SNP array genotyping of pooled extremes.

High-throughput SNP array analysis of pooled extreme phenotypes in a segregating population by KASP marker genotyping permitted rapid, cost-effective location of a stripe rust resistance QTL in wheat. German wheat cultivar "Friedrichswerther" has exhibited high levels of adult plant resistance (APR) to stripe rust in field environments for many years. F2:3 lines and F6 recombinant inbred line (RILs) populations derived from a cross between Friedrichswerther and susceptible landrace Mingxian 169 were evaluated in the field in 2013, 2016 and 2017. Illumina 90K iSelect SNP arrays were used to genotype bulked extreme pools and parents; 286 of 1135 polymorphic SNPs were identified on chromosome 6B. Kompetitive Allele-Specific PCR (KASP) markers were used to verify the chromosome region associated with the resistance locus. A linkage map was constructed with 18 KASP-SNP markers, and a major effect QTL was identified within a 1.4cM interval flanked by KASP markers IWB71602 and IWB55937 in the region 6BL3-0-0.36. The QTL, named QYr.nwafu-6BL, was stable across environments, and explained average 54.4 and 47.8% of the total phenotypic variation in F2:3 lines and F6 RILs, respectively. On the basis of marker genotypes, pedigree analysis and relative genetic distance QYr.nwafu-6BL is likely to be a new APR QTL. Combined high-throughput SNP array genotyping of pooled extremes and validation by KASP assays lowers sequencing costs compared to genome-wide association studies with SNP arrays, and more importantly, permits rapid isolation of major effect QTL in hexaploid wheat as well as improving accuracy of mapping in the QTL region. QYr.nwafu-6BL with flanking KASP markers developed and verified in a subset of 236 diverse lines can be used in marker-assisted selection to improve stripe rust resistance in breeding programs.

Design of character-based DNA barcode motif for species identification: A computational approach and its validation in fishes.

The DNA barcodes are generally interpreted using distance-based and character-based methods. The former uses clustering of comparable groups, based on the relative genetic distance, while the latter is based on the presence or absence of discrete nucleotide substitutions. The distance-based approach has a limitation in defining a universal species boundary across the taxa as the rate of mtDNA evolution is not constant throughout the taxa. However, character-based approach more accurately defines this using a unique set of nucleotide characters. The character-based analysis of full-length barcode has some inherent limitations, like sequencing of the full-length barcode, use of a sparse-data matrix and lack of a uniform diagnostic position for each group. A short continuous stretch of a fragment can be used to resolve the limitations. Here, we observe that a 154-bp fragment, from the transversion-rich domain of 1367 COI barcode sequences can successfully delimit species in the three most diverse orders of freshwater fishes. This fragment is used to design species-specific barcode motifs for 109 species by the character-based method, which successfully identifies the correct species using a pattern-matching program. The motifs also correctly identify geographically isolated population of the Cypriniformes species. Further, this region is validated as a species-specific mini-barcode for freshwater fishes by successful PCR amplification and sequencing of the motif (154bp) using the designed primers. We anticipate that use of such motifs will enhance the diagnostic power of DNA barcode, and the mini-barcode approach will greatly benefit the field-based system of rapid species identification.

Identification and characterization of Memecylon species using isozyme profiling

Background:The protein/isozyme fingerprint is useful in differentiating the species and acts as a biochemical marker for identification and systematic studies of medicinal plant species.Objective:In the present study, protein and isozyme profiles for peroxidase, esterase, acid phosphatase, polyphenol oxidase, alcohol dehydrogenase, and alkaline phosphatase of five species of Memecylon (Melastomataceae), Memecylon umbellatum, Memecylon edule, Memecylon talbotianum, Memecylon malabaricum, and Memecylon wightii were investigated.Materials and Methods:Fresh leaves were used to prepare crude enzyme extract for analyzing the five enzymes isozyme variations. Separation of isozymes was carried out using polyacrylamide gel electrophoresis (PAGE) and the banding patterns of protein were scored. Pair-wise comparisons of genotypes, based on the presence or absence of unique and shared polymorphic products, were used to regenerate similarity coefficients. The similarity coefficients were then used to construct dendrograms, using the unweighted pair group method with arithmetic averages.Results:A total of 50 bands with various Rf values and molecular weight were obtained through PAGE analysis. Among the five Memecylon species, more number of bands was produced in M. wightii and less number of bands was observed in M. edule. The results of similarity indices grouped M. malabaricum and M. wightii in one cluster with 98% similarity and M. umbellatum, M. edule, and M. talbotianum are grouped in another cluster with 79% similarity showing close genetic similarities which is in accordance with the morphological identification of Memecylon species.Conclusion:The protein/isozyme fingerprint is useful in differentiating the species and acts as a biochemical marker for identification of Memecylon species.SUMMARY Biochemical characterization of Memecylon species was evaluated by SDS-PAGE of extracted protein and isozyme profiling on native PAGE.After electrophoresis, each gel was stained with specific stains. Genetic distance relationships were evaluated based on the banding patterns of protein on isozymes.Unique banding pattern of esterase, peroxidase, acid phosphatase, alcohol dehydrogenase and polyphenol oxidase are observed in all the five species of Memecylon, which represent the fingerprint of Memecylon species.SDS-PAGE and isozyme profiling of five Memecylon species revealed that M. malabaricum and M. wightii grouped in one cluster and M. umbellatum, M. edule and M. talbotianum grouped in another cluster showing close genetic similarities which is in accordance with the morphological identification of Memecylon species.This is the first report on the comparison of protein and isozyme profile of five different Memecylon species. Abbreviations Used: SDS-PAGE: Sodium docecyl sulfate polyacrylamide gel electrophoresis; NTSYS PC2: Numerical taxonomy system, version 2.2 for Windows XP, Vista, Win7, Win 8 and Win10 including 64 bit

梧州繁殖中心圈养黑叶猴遗传多样性分析和野外放归种源选择

Mitochondrial DNA (mtDNA) control region and microsatellite DNA sequences were used to analyze genetic diversity, origins, and relationships of captive langur ( Trachypithecus francoisi ) individuals. Sequencing of the 355-bp mtDNA control region for 52 individuals uncovered 35 variable nucleotide sites, including 3 transitions (ts), 29 transversions (tv), and 3 insertion/deletions, with 13 defined haplotypes. A haplotype diversity of 0.627 and a nucleotide diversity of 0.027 were calculated. Eleven microsatellite loci showing good amplification were also assayed in the 52 individuals. A total of 47 alleles were detected, with an average of 4.18 per locus. Mean polymorphic information content ( PIC ) was 0.566. Expected heterozygosity ( He ) and observed heterozygosity ( Ho ) were 0.559 and 0.551. Compared with other endangered primates, we found that the genetic diversity of the captive T. francoisi population was not low. Based on phylogenetic analysis of haplotypes of wild and captive T. francoisi individuals, we inferred that the captive T. francoisi individuals came from Guangxi, near the Vietnamese border. Using genetic distance relationships, we selected three male and seven female captive langurs to establish three family units for reintroduction.

Metroglyph analysis of maize (Zea mays L.) inbreds for preliminary classification and group constellation

When a large number of accessions are available it is often useful to represent them on two dimensional graph and form preliminary groups which are subsequently subjected to more detailed stratification for specific breeding purposes. In the present investigation inbreds were grouped in to clusters using metroglyph analysis. Index scores were assigned to each glyph to arrive at conclusions about the agronomic potential of the inbreds. The group constellation deviated from the one derived through D2 analysis. However, pictorial representation of inbreds as brought about by metroglyph analysis can be used as a measure of relative genetic distance among the inbreds. Key words: D2 statistic, genetic divergence, group constellation, metroglyph analysis.

Genetic Contribution of Lumai 14 to Novel Wheat Varieties Developed in Shandong Province

Lumai 14 is a semi-dwarf high-yield wheat variety developed in the mid of 1980s,which is also a backbone parent of more than 40 wheat varieties released in China.This study aimed to understand the genetic contribution of Lumai 14 to its derivate varieties and lines at the genomic level.Using 350 SSR markers covering the whole wheat genome,the alleles of Lumai 14 were screened in six Lumai 14 derivants and Yannong 15(another parent of Qingfeng series).A total of 662 alleles were obtained on the 350 loci,and each locus had 1-5 alleles with an average of 1.9 alleles.The polymorphism information content(PIC) was 0.21.In the UPGMA dendrogram,Jimai 22 and Lumai 14 were clustered together firstly,and further grouped with Qingfeng series.Jimai 20 showed relative large genetic distance to the backbone parent.The derivants of Lumai 14 shared common loci with their parents with percentages of 67.1%(235/350) for Jimai 22,60.0%(210/350) for Jimai 20,65.4%(229/350) for Qingfeng 1,and 70.6%(247/350) for Qingnong 2.Most of these loci were assembled on 21 chromosomes,and some of them,such as regions gwm304-barc360-gwm415-barc1 on chromosome 5A and barc196-gdm127-barc123 on chromosome 6D,were shared in six Lumai 14 derivants.In Jimai 22,alleles inherited from Lumai 14 varied among chromosomes,and chromosomes 3A,4A,7A,2B,4B,7B,1D,3D,and 4D contained more than 70% of Lumai 14 alleles,whereas chromosome 3B showed the lowest percentage of 46%.These alleles from Lumai 14 were mainly distributed in several regions on each chromosome,which proved to harbor genes/QTLs for important traits in QTL analysis and association analysis.Therefore,we conclude that the elite background of Lumai 14 contributed greatly to Jimai 22.In breeding practices,background selection should be highly considered besides the transmission of elite target genes.

Construction of an insertion marker collection of Sz. japonicus (IMACS) for genetic mapping and a fosmid library covering its genome

Measuring relative genetic distances is one of the best ways to locate genetic loci. Here we report the construction of a strains set for genetic mapping in Schizosaccharomyces japonicus, which belongs to the genus Schizosaccharomyces together with the well-studied fission yeast Sz. pombe. We constructed 29 strains that bear a positive-negative selection marker at different loci. The marker was inserted every 500 kb in the genome of Sz. japonicus. Each marker thus becomes a 'scale mark' of a chromosome that behaves like a yardstick. By determining the genetic distances from the inserted markers, the relative location of a genomic mutation can be determined. We also constructed a fosmid library that covers an entire genome of Sz. japonicus. These tools together would facilitate identification and cloning of the gene.

Genetic differentiation between Cinta Senese and commercial pig breeds using microsatellite

Background: Cinta Senese is an autochthonous Tuscan breed, which risked extinction since the ‘60s. Results: Monitoring the genetic variability of the actual population by use of DNA molecular markers is essential to address a correct breeding policy, finalized to obtain the race preservation and its fitness in the future. 17 SSRs autosomal markers and 1 associated to the X chromosome were used to genotype 86 individuals belonging to the CS and 12 belonging to two main white races L, LW and crosses between LW and L and L and CS widespread in Tuscany and used in the recent past to obtain hybrids with the CS. Conclusions: A dendrogram of similarity measures the relative genetic distance between individuals in the population. Data show that CS pigs have a distinct genotype from L, LW, LW x L and L x CS.

Differentiation and classification of phytoplasmas in the pigeon pea witches’-broom group (16SrIX): an update based on multiple gene sequence analysis

The pigeon pea witches'-broom phytoplasma group (16SrIX) comprises diverse strains that cause numerous diseases in leguminous trees and herbaceous crops, vegetables, a fruit, a nut tree and a forest tree. At least 14 strains have been reported worldwide. Comparative phylogenetic analyses of the highly conserved 16S rRNA gene and the moderately conserved rplV (rpl22)-rpsC (rps3) and secY genes indicated that the 16SrIX group consists of at least six distinct genetic lineages. Some of these lineages cannot be readily differentiated based on analysis of 16S rRNA gene sequences alone. The relative genetic distances among these closely related lineages were better assessed by including more variable genes [e.g. ribosomal protein (rp) and secY genes]. The present study demonstrated that virtual RFLP analyses using rp and secY gene sequences allowed unambiguous identification of such lineages. A coding system is proposed to designate each distinct rp and secY subgroup in the 16SrIX group.