Rapid Constructing a Genetic Linkage Map by AFLP Technique and Mapping a New Gene tms5

In this study, we reported the repaid construction of a molecular marker linkage map of rice (Oryza sativa L.). An F-2 population from the cross between Annong S-1 and Nanjing 11 was used to construct a genetic linkage map of rice. Total of 142 newly screened AFLP markers and 30 anchor markers (25 SSR markers and 5 RFLP markers) were mapped on the 12 chromosomes covering 1537.4 cM of rice genome. The average interval between these markers was 9.0 cM. The total work which usually was finished in more than one year was finished within only 3 months by one person. This is the first plant AFLP map developed in China. A new thermosensitive genic male sterile gene in rice, tms5, was Egged and mapped onto chromosome 2 during the development of the linkage map.

Construction of Molecular Genetic Linkage Map Based on an RIL Population of Rice and Detection of QTLs for Tiller Angle

In this study, an RIL （recombinant inbred line） population containing 240 lines was developed by single seed descent method （SSD） based on a parent com- bination of small-grain indica cultivar Kasalath and large-grain japanica cultivar TD70 with significant differences in plant type traits, to construct the molecular genetic linkage map. Totally 838 SSR （Simple Sequence Repeat） markers were used for polymorphism screening between parents, 302 SSR markers with polymorphism were detected, with a frequency of 36.04%; 141 SSR markers with clear amplified bands and uniform distribution in the genome were finally used for genotype analysis of the RIL population. According to the experimental results, the frequency of male and female genotype in this RIL population was respectively 53% and 47%, suggesting good balance in population structure. A molecular genetic linkage map of rice was constructed by 141 markers based on a RIL population of 240 lines, with a total genetic distance of about 1 832.47 cM covering all 12 chromosomes, an average genetic distance between markers of 12.70 cM and a range of genetic distance be- tween markers of 0.43-36.11 cM, which is consistent with basic requirements of quantitative trait locus （QTL） mapping. Except for few markers on chromosomes 1 and 8, the order and location of markers is similar to the published sequences of Nipponbare. QTL analysis for the tiller angle was conducted with this RIL population of 240 lines, and results showed that three QTLs controlling tiller angle were detected on chromosome 8, 9 and 11, which were named qTA8, qTA9 and qTA11, with a contribution rate of 4.10%, 26.08% and 4.35%, respectively. To be specific, qTA9 contained Tiller Angle Controlling （TAC1） gene. The construction of this molecular genetic linkage map laid the foundation for genetic analysis and QTL mapping of various traits in the progeny of indica and japonica.

Construction of Genetic Linkage Map Based on SSR Markers in Peanut(Arachis hypogaea L.)

Molecular genetic maps of crop species can be used in a variety of ways in breeding and genomic research such as identification and mapping of genes and quantitative trait loci （QTLs） for morphological, physiological and economic traits of crop species. However, a comprehensive genetic linkage map for cultivated peanut has not yet been developed due to the extremely low frequency of DNA polymorphism in cultivated peanut. In this study, 142 recombinant inbred lines （RILs） derived from a cross between Yueyou 13 and Zhenzhuhei were used as mapping population in peanut （Arachis hypogaea L.）. A total 652 pairs of genomic-SSR primer and 392 pairs of EST-SSR primer were used to detect the polymorphisms between the two parents. 141 SSR primer pairs, 127 genomic-SSR and 14 EST-SSR ones, which can be used to detect polymorphisms between the two parents, were selected to analyze the RILs population. Thus, a linkage genetic map which consists of 131 SSR loci in 20 linkage groups, with a coverage of 679 cM and an average of 6.12 cM of inter-maker distance was constructed. The putative functions of 12 EST-SSR markers located on the map were analyzed. Eleven showed homology to gene sequences deposited in GenBank. This is the first report of construction of a comprehensive genetic map with SSR markers in peanut （Arachis hypogaea L.）. The map presented here will provide a genetic framework for mapping the qualitative and quantitative trait in peanut.

A genetic linkage map with 178 SSR and 1901 SNP markers constructed using a RIL population in wheat (Triticum aestivum L.)

The construction of high density genetic linkage map provides a powerful tool to detect and map quantitative trait loci(QTLs) controlling agronomically important traits. In this study, simple sequence repeat(SSR) markers and Illumina 9K i Select single nucleotide polymorphism(SNP) genechip were employed to construct one genetic linkage map of common wheat(Triticum aestivum L.) using 191 recombinant inbred lines(RILs) derived from cross Yu 8679×Jing 411. This map included 1 901 SNP loci and 178 SSR loci, covering 1 659.9 c M and 1 000 marker bins, with an average interval distance of 1.66 c M. A, B and D genomes covered 719.1, 703.5 and 237.3 c M, with an average interval distance of 1.66, 1.45 and 2.9 c M, respectively. Notably, the genetic linkage map covered 20 chromosomes, with the exception of chromosome 5D. Bioinformatics analysis revealed that 1 754(92.27%) of 1 901 mapped SNP loci could be aligned to 1 215 distinct wheat unigenes, among which 1 184(97.4%) were located on o ne single chromosome, and the rest 31(2.6%) were located on 2 to 3 chromosomes. By performing in silico comparison, 214 chromosome deletion bin-mapped expressed sequence tags(ESTs), 1 043 Brachypodium genes and 1 033 rice genes were further added onto the genetic linkage map. This map not only integrated genetic and physical maps, SSR and SNP loci, respectively, but also provided the information of Brachypodium and rice genes corresponding to 1 754 SNP loci. Therefore, it will be a useful tool for comparative genomics analysis, fine mapping of QTL/gene controlling agronomically important traits and marker-assisted selection breeding in wheat.

A Genetic Linkage Map of Brassica campestris L.ssp. pekinensis (syn. B. rapa L. ssp. pekinensis)

A molecular genetic map of Chinese cabbage was constructed with a 102 recombinant inbred (RI) population from a cross of two cultivated Chinese cabbage lines 177 and 276, using AFLP and RAPD markers. 352 markers including 265 AFLP markers and 87 RAPD markers were integrated into 17 linkage groups. It covered a total of 2 665. 7 cM with an average interval of 7. 6 cM. AFLP marker is efficient for map construction while it easily forms clusters to cause big gaps in map. A total of 13.92 % abnormal segregation markers distributed in the map. The molecular genetic map is fundamental for gene localization, comparative genomics, and QTL mapping of important agronomic traits.

Constructing the wolfberry(Lycium spp.) genetic linkage map using AFLP and SSR markers

Genetic linkage maps are important for quantitative trait locus(QTL) and marker-assisted selection breeding. The wolfberry(Lycium spp.) is an important food and traditional medicine in China. However, few construction genetic linkage maps have been reported because of the lack of genomic and genetic resources. In this study, a population of 89 F1 seedings was derived from a cross between two heterozygous parents, L. chinense var. potaninii ‘BF-01’(female)and L. barbarum var. auranticarpum ‘NH-01’(male), in order to construct a genetic linkage map using simple sequence repeat(SSR) and amplified fragment length polymorphism(AFLP) markers based on the double pseudo-test cross mapping strategy. The resulting genetic map consisted of 165 markers(74 AFLPs and 91 SSRs) distributed across 12 linkage groups and spanned a total length of 557.6 cM with an average distance of 3.38 cM between adjacent markers.The 12 linkage groups contained 3 to 21 markers and ranged in length from 8.6 to 58.3 cM. Twenty-nine segregated markers distributed in the map were mainly located on LG4 and LG9 linkage groups at P<0.05. This is the first linkage map of Lycium species using SSR and AFLP markers, which can serve as basis for improving genes and selective breeding of the genome assembly.

A Microsatellite Genetic Linkage Map of Black Rockfish(Sebastes schlegeli)

Ovoviviparous black rockfish(Sebastes schlegeli) is an important marine fish species for aquaculture and fisheries in China. Genetic information of this species is scarce because of the lack of microsatellite markers. In this study, a large number of microsatellite markers of black rockfish were isolated by constructing microsatellite-enriched libraries. Female- and male-specific genetic linkage maps were constructed using 435 microsatellite markers genotyped in a full-sib family of the fish species. The female linkage map contained 140 microsatellite markers, in which 23 linkage groups had a total genetic length of 1334.1 c M and average inter-marker space of 13.3 c M. The male linkage map contained 156 microsatellite markers, in which 25 linkage groups had a total genetic length of 1359.6 c M and average inter-marker distance of 12.4 c M. The genome coverage of the female and male linkage maps was 68.6% and 69.3%, respectively. The female-to-male ratio of the recombination rate was approximately 1.07:1 in adjacent microsatellite markers. This paper presents the first genetic linkage map of microsatellites in black rockfish. The collection of polymorphic markers and sex-specific linkage maps of black rockfish could be useful for further investigations on parental assignment, population genetics, quantitative trait loci mapping, and marker-assisted selection in related breeding programs.

QTL Mapping for Fiber Quality Traits Based on a Dense Genetic Linkage Map with SSR,TRAP,SRAP and AFLP Markers in Cultivated Tetraploid Cotton

Cotton is one of the most important economic crops in the world,and it provides natural fiber for the textile industry.With the advancement of the textile technology and increased consumption demands on cotton fiber,both cotton yield and quality should be enhanced.However,cotton yield

Constructing Genetic Linkage Maps Using the Whole Genome Sequence of Pacific Bluefin Tuna (Thunnus orientalis) and a Comparison of Chromosome Structure among Teleost Species

Pacific bluefin tuna (Thunnus orientalis) is one of the most economically important species in the Percomorpha group of teleost fishes. Their migrations are extensive and depend upon continuous swimming at a high rate of speed throughout their life. The draft genome sequence of this species has been reported but remains highly fragmented. We constructed a Pacific bluefin tuna genetic linkage map using microsatellite markers developed on each of the scaffolds from the draft genome sequence to link these genome fragments and understand the genomic structure of species in Percomorpha. Of the 606 polymerase chain reaction microsatellite primer pairs tested, 473 were polymorphic in the mapping populations for the linkage analysis. We constructed sex-specific maps for 24 linkage groups consisting of 470 markers, which allowed us to place scaffolds that cumulatively represented 20.8% (153.8 Mb) of the sequenced genome onto the linkage groups. The distribution of orthologous genes on the chromosomes of tuna and four other teleost fish species suggested that the constitution of tuna chromosomes is closest to that of medaka. Both species have the 24 chromosomes of the ancestral teleost, including several chromosomal inversions. The integrated map developed in this study will be useful to construct a complete physical map to conduct comparative teleost genomics and genetic studies on economically useful traits in Pacific bluefin tuna.

SHEsis,a powerful software platform for analyses of linkage disequi-librium,haplotype construction,and genetic association at polymor-phism loci

The authors want to changed the web link of the software platform in this Briefing.Page 97,section 'INTRODUCTION',the web link of SHEsis is changed from http://www.nhgg.org/analysis tohttp://analysis.bio-x.

Complete Real Solution of the Five-orientation Motion Generation Problem for a Spherical Four-bar Linkage

For a spherical four-bar linkage,the maximum number of the spherical RR dyad（R：revolute joint）of five-orientation motion generation can be at most 6.However,complete real solution of this problem has seldom been studied.In order to obtain six real RR dyads,based on Strum＇s theorem,the relationships between the design parameters are derived from a 6th-degree univariate polynomial equation that is deduced from the constraint equations of the spherical RR dyad by using Dixon resultant method.Moreover,the Grashof condition and the circuit defect condition are taken into account.Given the relationships between the design parameters and the aforementioned two conditions,two objective functions are constructed and optimized by the adaptive genetic algorithm（AGA）.Two examples with six real spherical RR dyads are obtained by optimization,and the results verify the feasibility of the proposed method.The paper provides a method to synthesize the complete real solution of the five-orientation motion generation,which is also applicable to the problem that deduces to a univariate polynomial equation and requires the generation of as many as real roots.

Construction of high-density genetic linkage map of Pyropia yezoensis(Bangiales,Rhodophyta)and identifi cation of red color trait QTLs in the thalli

Pyropia yezoensis is an important macroalga because of its extensive global distribution and economic importance.Color is an important trait in the thalli of P.yezoensis,it is also an effective marker to identify the hybridization in genetic breeding.In this study,a high-density genetic linkage map was constructed based on high-throughput single nucleotide polymorphism(SNP)markers,and used for analyzing the quantitative trait loci(QTLs)of red color trait in the thalli of P.yezoensis.The conchospore undergoes meiosis to develop into an ordered tetrad,and each cell has a haploid phenotype and can grow into a single individual.Based on this theory,F1 haploid population was used as the mapping population.The map included 531 SNP markers,394.57 cM long on average distance of 0.74 cM.Collinear analysis of the genetic linkage map and the physical map indicated that the coverage between the two maps was 79.42%.Furthermore,QTL mapping identified six QTLs for the chromosomal regions associated with the red color trait of the thalli.The value of phenotypic variance explained(PVE)by an individual QTL ranged from 4.71%-63.11%.And QTL qRed-1-1,with a PVE of 63.11%,was considered the major QTL.Thus,these data may provide a platform for gene and QTL fine mapping,and marker-assisted breeding in P.yezoensis in the future.

Genetic Linkage Analysis of the Natural Colored Fiber and Fuzzless Traits in Cotton

Genetic linkage relationship of the natural colored fiber and six fuzzless seed germplasms in obsolete backgrounds of Gossypium hirsutum(AD genome) and G.barbadense were analyzed in the

Preliminary genetic linkage map of the abalone Haliotis diversicolor Reeve

Haliotis diversicolor Reeve is one of the most important mollusks cultured in South China. Preliminary genetic linkage maps were constructed with amplified fragment length polymorphism (AFLP) markers. A total of 2 596 AFLP markers were obtained from 28 primer combinations in two parents and 78 offsprings. Among them, 412 markers (15.9%) were polymorphic and segregated in the mapping family. Chi-square tests showed that 151 (84.4%) markers segregated according to the expected 1:1 Mendelian ratio (P<0.05) in the female parent, and 200 (85.8%) in the male parent. For the female map, 179 markers were used for linkage analysis and 90 markers were assigned to 17 linkage groups with an average interval length of 25.7 cm. For the male map, 233 markers were used and 94 were mapped into 18 linkage groups, with an average interval of 25.0 cm. The estimated genome length was 2 773.0 cm for the female and 2 817.1 cm for the male map. The observed length of the linkage map was 1 875.2 cm and 1 896.5 cm for the female and male maps, respectively. When doublets were considered, the map length increased to 2 152.8 cm for the female and 2 032.7 cm for the male map, corresponding to genome coverage of 77.6% and 72.2%, respectively.

Genetic Linkage Map and Comparative Genome Analysis for the Atlantic Killifish (Fundulus heteroclitus)

Genetic linkage maps are valuable tools in evolutionary biology;however, their availability for wild populations is extremely limited. Fundulus heteroclitus (Atlantic killifish) is a non-migratory estuarine fish that exhibits high allelic and phenotypic diversity partitioned among subpopulations that reside in disparate environmental conditions. An ideal candidate model organism for studying gene-environment interactions, the molecular toolbox for F. heteroclitus is limited. We identified hundreds of novel microsatellites which, when combined with existing microsatellites and single nucleotide polymorphisms (SNPs), were used to construct the first genetic linkage map for this species. By integrating independent linkage maps from three genetic crosses, we developed a consensus map containing 24 linkage groups, consistent with the number of chromosomes reported for this species. These linkage groups span 2300 centimorgans (cM) of recombinant genomic space, intermediate in size relative to the current linkage maps for the teleosts, medaka and zebrafish. Comparisons between fish genomes support a high degree of synteny between the consensus F. heteroclitus linkage map and the medaka and (to a lesser extent) zebrafish physical genome assemblies.

Inheritance of AFLP markers and genetic linkage analysis in two full-sib families of the marine shrimp Litopenaeus vannamei(Crustacea,Decapoda)

The cultivation of the marine species of shrimp Litopenaeus vannamei has emerged as one of the segments that best develop in the Brazilian aquaculture, representing the agribusiness that grew the most in recent years. Regarding the economic importance of the farming of this species in Brazil, further studies on genetic improvement were conducted. A F2 segregating population consisting of 192 samples for each G1 and G2 families, from crossing inbred lines was used for the studies performed in the present work. The genetic linkage analysis was based on polymorphic markers derived from nine AFLP (Amplified Fragment Length Polymorphism) primers. Fourteen genetic linkage groups including 103 segregating polymorphic markers were constructed covering350 cMfor G1 and four genetic linkage groups including 59 markers were constructed covering300 cMfor G2. Simple marker analyses were performed among individuals evaluated phenotypically, finding markers linked to genes that may be potentially important and useful to assess characteristics of economic importance for traits related to weight and the disease IMN (idiopathic muscle necrosis). The statistical model including markers explained major proportion of phenotypic characteristic weight in relation to disease incidence IMN.

Construction of SNP genetic maps based on targeted next-generation sequencing and QTL mapping of vital agronomic traits in faba bean(Vicia faba L.)

Owing to the limitation of a large genome size(~13 Gb),the genetic and gene mapping studies on faba bean(Vicia faba L.)are lagging far behind those for other legumes.In this study,we selected three purified faba bean lines(Yundou 8137,H0003712,and H000572)as parents and constructed two F2 populations.These two F2 populations,namely 167 F2 plants in Pop1(Yundou 8137×H0003712)and 204 F2 plants in Pop2(H000572×Yundou 8137),were genotyped using a targeted next-generation sequencing(TNGS)genotyping platform,and two high-density single nucleotide polymorphisms(SNP)genetic linkage maps of faba bean were constructed.The map constructed from Pop1 contained 5103 SNPs with a length of 1333.31 cM and an average marker density of 0.26 cM.The map constructed from Pop2 contained 1904 SNPs with a greater length of 1610.61 cM.In these two F2 populations,QTL mapping identified 98 QTLs for 14 agronomic traits related to the flowers,pods,plant types and grains.The two maps were then merged into an integrated genetic linkage map containing 6895 SNPs,with a length of 3324.48 cM.These results not only lay the foundation for fine mapping and map-based cloning of related genes,but can also accelerate the molecular marker-assisted breeding of faba bean.

QTL Analysis of Traits Related to Melon Stigma and Ovary Size

The melon varieties MR-1 and M4-7 were used as the parent materials to produce hybrids.A total of 170 F2 individuals were used as the mapping population to construct a genetic linkage map.In this study,240 cleaved amplified polymorphism sequence(CAPS)molecular markers were developed,and 105 of which showed polymorphism between parents.The map contained 105 markers grouped into 12 linkage groups,spanning a total length of 1998.85 cM,with an average length of 19.04 cM between markers.The composite interval mapping(CIM)method was used to detect QTLs related with melon stigma and ovary traits:stigma longitudinal diameter(STLD),stigma transverse diameter(STTD),stigma weight(STW),ovary longitudinal diameter(OLD),and ovary transverse diameter(OTD).A total of nine QTLs were identified:six for stigma size and three for ovary size.A total of six loci were detected for stigma size,which included two loci for stigma longitudinal diameter,two loci for stigma transverse diameter,and two loci for stigma weight.The major effective locus regulating stigma transverse diameter was qSTTD-9-1.A total of three loci were identified for ovary size traits,including one locus for ovary longitudinal diameter and two loci for ovary transverse diameter.

Quantitative Trait Loci(QTL)Mapping and Marker Analysis of Fatty Acids in Peanut

Peanut,with high oil content,has been a major oil and food crop globally.The compositions of the fatty acids are the common factors in determining the oil quality.In the present study,an F2 segregated population with 140 individuals derived from the cross of Weihua8(a cultivar)and 12L49(a line with high oleic acid concentration)was used to construct a genetic map and conduct QTL mapping analysis.A total of 103 polymorphic SSR primers were utilized for genotyping the RILs and finally generating the SSR loci.Within the 103 SSR loci,a genetic linkage map,covering a total length of 3592.35 cM of the whole peanut genome,was constructed.Based on the genetic map,sixteen QTLs located on nine linkage groups related to peanut fatty acids were finally identified.Among them,four QTLs were detected associated with various traits simultaneously,which showed genetic stability in relation to fatty acids of peanut.Except for the QTLs for oleic acid,linoleic acid,and linolenic acid,three novel QTLs for arachidic acid and behenic acid were also detected.These QTLs might be helpful for further fine mapping analysis and marker-assisted selection of fatty acids in peanut.

Differences in Ecological Fitness Between Bt Transgenic Rice and Conventional Rice Under Insect-infestation Pressures

[Objective] This study aimed to improve density and practicality of the ge- netic map of sunflower （Helianthus annuus L.） by adding some SSR markers. [Method] A total of 123 F8 RILs populations derived from a cross between PAC-2 and RHA-266 were selected as the materials, and a total of 300 pairs of SSR primers were used to screen polymorphic markers between the parents and some of their RILs, and finally 51 pairs of the primers producing polymorphic patterns were selected to construct the genetic map of the RILs populations. [Result] Nineteen pairs of SSR primers did not generate polymorphic patterns or any bands, and 32 SSR pairs showed polymorphism. Thirty-five alleles which distributed in the 15 link- age groups of the maps were detected. The new map covered a total length of 2 914.5 cM, 7.5 cM longer than that of the original map. The average marker interval is 8.1 cM replacing original 9.0 cM. [Conclusion] This study provided reference for genetic map integration and molecular marker assisted selection of sunflower.