Mapping of Quantitative Trait Loci Affecting Eggshell Quality in an F2 Population Derived from Strong and Weak Eggshell Lines of the White Leghorn Chicken Breed

Broken and cracked eggshells cause major economic losses to the egg production industry. An F2 population of 262 hens obtained by crossing a strong egg shell line with a weak egg shell line of the White Leghorn breed was used for detecting the quantitative trait loci （QTL） affecting eggshell quality. The 2 lines were developed from the same founder population by two-way selection for egg shell strength with nondestructive deformation. Of the 1 014 microsatellite markers tested, 35 were mapped on 10 autosomal linkage groups. There was no informative marker on chromosome Z. The QTLs associated with 7 traits, i.e., body weight, short length of egg, long length of egg, eggshell strength, eggshell thickness （EST）, eggshell weight （ESW）, and egg weight （EW）, were identified. Highly significant （P〈0.01） QTLs associated with EST and ESW and a significant （P〈 0.05） QTL associated with EW were mapped to a region flanking ABR0545 and ABR0362 on chromosome 9. These QTLs are good candidates to be employed in the development of strategies for reducing the number of broken and cracked eggs in commercial layer houses by employing marker assisted selection.     

An Integrated QTL Map of Fungal Disease Resistance in Soybean （G/ycine max L. Merr）： A Method of Meta-Analysis for Mining R Genes

Diseases caused by fungal pathogens account for approximately 50% of all soybean disease losses around the world. Conflicting results of fungal disease resistance QTLs from different populations often occurred. The objectives of this study were to： （i） evaluate evidence for reported fungal disease resistance QTLs associations in soybean and （ii） extract relatively reliable and useful information from the ＂real＂ QTLs and mine putative genes in soybean. An integrated map of fungal disease resistance QTLs in soybean was established with soymap 2 published in 2004 as a reference map. QTLs of fungal disease resistance developed from each of separate populations in recent 10 years were integrated into a combinative map for gene cloning and marker assisted selection in soybean. 107 QTLs from different maps were integrated and projected to the reference map with the software BioMercator 2.1. A method of meta-analysis was used to narrow down the confidence interval, and 23 ＂real＂ QTLs and their corresponding markers were obtained from 12 linkage groups （LG）, respectively. Two published R genes were found in these ＂real＂ QTLs intervals. Sequences in the ＂real＂ QTLs intervals were predicted by GENSCAN, and these predicted genes were annotated in Goblet. 228 resistance gene analogs （RGAs） in 12 different terms were mined. The results will lay the foundation for a bioinformatics platform combining abundant QTLs, and offer the basis for marker assisted selection and gene cloning in soybean.     

QTL Analysis of the Oil Content and the Hull Content in Brassica napus L.

The QTLs of the oil content and the hull content were analyzed in Brassica napus L. By constructing the linkage map. The F26 RIL population with 188 lines, derived from the cross of GH06 × P147, was used as the mapping population. The SRAP, SSR, AFLP, and TRAP markers were used to construct the linkage map, and the composite interval mapping (CIM) to identify the quantitative trait loci associated with the oil content and the hull content. 300 markers were integrated into 19 linkage groups, covering 1 248.5 cM in total. Seven QTLs were found to be responsible for the oil content with the single contribution to phenotypic variance ranging from 3.73 to 10.46%; four QTLs were found for the hull content with the single contribution to phenotypic variance ranging from 4.89 to 6.84%. The yellow-seeded Brassica napus L. Has the advantage of higher oil content and the hull content has a significant effect on the oil content. In addition, the SRAP marker is good for detecting QTL.     

Identification of QTLs for Starch Content in Sweetpotato （Ipomoea batatas （L.） Lam.）

Sweetpotato （Ipomoea batatas （L.） Lam.） breeding is challenging due to its genetic complexity. In the present study, interval mapping （IM） and multiple quantitative trait locus （QTL） model （MQM） analysis were used to identify QTLs for starch content with a mapping population consisting of 202 F1 individuals of a cross between Xushu 18, a cultivar susceptible to stem nematodes, with high yield and moderate starch, and Xu 781, which is resistant to stem nematodes, has low yield and high starch content. Six QTLs for starch content were mapped on six linkage groups of the Xu 781 map, explaining 9.1-38.8% of the variation. Especially, one of them, DMFN 4, accounted for 38.8% of starch content variation, which is the QTL that explains the highest phenotypic variation detected to date in sweetpotato. All of the six QTLs had a positive effect on the variation of the starch content, which indicated the inheritance derived from the parent Xu 781. Two QTLs for starch content were detected on two linkage groups of the Xushu 18 map, explaining 14.3 and 16.1% of the variation, respectively. They had a negative effect on the variation, indicating the inheritance derived from Xu 781. Seven of eight QTLs were co-localized with a single marker. This is the first report on the development of QTLs co-localized with a single marker in sweetpotato. These QTLs and their co-localized markers may be used in marker-assisted breeding for the starch content of sweetpotato.     

Identiifcation and Molecular Mapping of the RsDmR Locus Conferring Resistance to Downy Mildew at Seedling Stage in Radish （Raphanus sativus L.）

Downy mildew （DM）, caused by the fungus Peronospora parasitica, is a destructive disease of radish （Raphanus sativus L.） worldwide. Host resistance has been considered as an attractive and environmentally friendly approach to control the disease. However, the genetic mechanisms of resistance in radish to the pathogen remain unknown. To determine the inheritance of resistance to DM, F1, F2 and BC1F1 populations derived from reciprocal crosses between a resistant line NAU-dhp08 and a susceptible line NAU-qtbjq-06 were evaluated for their responses to DM at seedling stage. All F1 hybrid plants showed high resistance to DM and maternal effect was not detected. The segregation for resistant to susceptible individuals statistically iftted a 3：1 ratio in two F2 populations （F2（SR） and F2（RS））, and 1：1 ratio in two BC1F1 populations, indicating that resistance to DM at seedling stage in radish was controlled by a single dominant locus designated as RsDmR. A total of 1 972 primer pairs （1 036 SRAP, 628 RAPD, 126 RGA, 110 EST-SSR and 72 ISSR） were screened, and 36 were polymorphic between the resistant and susceptible bulks, and consequently used for genotyping individuals in the F2 population. Three markers （Em9/ga24370, NAUISSR826700 and Me7/em10400） linked to the RsDmR locus within a 10.0 cM distance were identiifed using bulked segregant analysis （BSA）. The SRAP marker Em9/ga24370 was the most tightly linked one with a distance of 2.3 cM to RsDmR. These markers tightly linked to the RsDmR locus would facilitate marker-assisted selection and resistance gene pyramiding in radish breeding programs.     

Inheritance and Molecular Mapping of Stripe Rust Resistance Gene Yr88375 in Chinese Wheat Line Zhongliang 88375

Stripe rust is one of the most important diseases of wheat worldwide. Inheritance of stripe rust resistance and mapping of resistance gene with simple sequence repeat （SSR） markers are studied to formulate efficient strategies for breeding cultivars resistant to stripe rust. Zhongliang 88375, a common wheat line, is highly resistant to all three rusts of wheat in China. The gene conferring rust disease was deduced originating from Elytrigia intermedium. Genetic analysis of Zhongliang 88375 indicated that the resistance to PST race CYR31 was controlled by a single dominant gene, temporarily designated as Yr88375. To molecular map Yr88375, a F2 segregating population consisting of 163 individuals was constructed on the basis of the hybridization between Zhongliang 88375 and a susceptible wheat line Mingxian 169; 320 SSR primer pairs were used for analyzing the genetic linkage relation. Six SSR markers, Xgwm335, Xwmc289, Xwmc810, Xgdmll6, Xbarc59, and Xwmc783, are linked to Yr88375 as they were all located on chromosome 5BL Yr88375 was also located on that chromosome arm, closely linked to Xgdmll6 and Xwmc810 with genetic distances of 3.1 and 3.9 cM, respectively. The furthest marker Xwmc783 was 13.5 cM to Yr88375. Hence, pedigree analysis of Zhongliang 88375 combined with SSR markers supports the conclusion that the highly resistance gene Yr88375 derived from Elytrigia intermedium is a novel gene for resistance to stripe rust in wheat. It could play an important role in wheat breeding programs for stripe rust resistance.     

QTL Mapping of Isoflavone,Oil and Protein Contents in Soybean （Glycine max L. Merr.）

Soybean （Glycine max L. Merr.） is the world＇s foremost source of edible plant oil and proteins, meantime, the biologically active secondary metabolites such as saponins and isoflavones are benefit to human health. The objective of this study was to identify quantitative trait loci （QTL） and epistatic interactions associated with isoflavone, protein, and oil contents in soybean seeds. An F13 recombinant inbred line （RIL） comprising 474 lines was derived from a cross between Jindou 23 and Huibuzhi cultivars. SSR technique was employed for mapping of the QTLs. The QTLs for isoflavone, protein, and oil contents were analyzed and 23 QTLs were detected based on the constructed linkage map. Six QTLs for isoflavone content were localized in linkage groups J, N, D2, and G, eleven QTLs for oil content were localized in the linkage groups A1, A2, B2, C2, and D2, and six QTLs for protein content were localized in linkage groups B2, C2, G, and H1. The correlative analysis demonstrated that the isoflavone content had significant correlation with protein content, while significantly negative correlations was existed between oil and protein content, and significantly positive correlations was existed between protein and oil content. All these findings have laid an important basis for the marker assisted breeding in soybean. The phenotypic correlations of quantitative traits may be resulted from the correlation of the QTL controlling those traits.     

Identification of QTLs for Starch Content in Sweetpotato(Ipomoea batatas(L.) Lam.)

Sweetpotato（Ipomoea batatas（L.）Lam.）breeding is challenging due to its genetic complexity.In the present study,interval mapping（IM）and multiple quantitative trait locus（QTL）model（MQM）analysis were used to identify QTLs for starch content with a mapping population consisting of 202 F1 individuals of a cross between Xushu 18,a cultivar susceptible to stem nematodes,with high yield and moderate starch,and Xu 781,which is resistant to stem nematodes,has low yield and high starch content.Six QTLs for starch content were mapped on six linkage groups of the Xu 781 map,explaining 9.1-38.8%of the variation.Especially,one of them,DMFN₄,accounted for 38.8%of starch content variation,which is the QTL that explains the highest phenotypic variation detected to date in sweetpotato.All of the six QTLs had a positive effect on the variation of the starch content,which indicated the inheritance derived from the parent Xu 781.Two QTLs for starch content were detected on two linkage groups of the Xushu 18 map,explaining 14.3 and 16.1%of the variation,respectively.They had a negative effect on the variation,indicating the inheritance derived from Xu 781.Seven of eight QTLs were co-localized with a single marker.This is the first report on the development of QTLs co-localized with a single marker in sweetpotato.These QTLs and their co-localized markers may be used in marker-assisted breeding for the starch content of sweetpotato.     

A Dominant Locus,qBSC-1, Controls β Subunit Content of Seed Storage Protein in Soybean（Glycine max（L.） Merri.）

Soybean seed storage protein is one of the most important plant vegetable proteins, and β subunit is of great significance to enhance soybean protein quality and processing property. F2 segregated population and residual heterozygous lines（RHL） derived from the cross between Yangyandou（low level of β subunit） and Zhonghuang 13（normal level of β subunit） were used for mapping of β subunit content. Our results showed that β subunit content was controlled by a single dominant locus, qBSC-1（β subunit content）, which was mapped to a region of 11.9 cM on chromosome 20 in F2 population of 85 individuals. This region was narrowed down to 2.5 cM between BARCSOYSSR_20_0997 and BARCSOYSSR_20_0910 in RHL with a larger population size of 246 individuals. There were 48 predicted genes within qBSC-1 region based on the reference genome（Glyma 1.0, Williams 82）, including the two copies of β subunit coding gene CG4. An InDel marker developed from a thymine（TT） insertion in one copy of CG4 promoter region in Yangyandou cosegregrated with BARCSOYSSR_20_0975 within qBSC-1 region, suggesting that this InDel marker maybe useful for marker-assisted selection（MAS）.     

Identification of QTLs Related to Bolting in Brassica rapa ssp. pekinensis(syn. Brassica campestris ssp. pekinensis)

A genetic linkage map of Brassica rapa ssp. pekinensis was constructed with 186 AFLP (amplified fragment length polymorphism) markers by using a doubled-haploid (DH) population with 183 individuals. The individuals were derived from F1 which was developed by crossing a bolting resistant DH line Y-177-12 and an easy bolting DH line Y195-93a.AFLPs were generated by the use of restriction enzymes EcoR Ⅰ and Mse Ⅰ. The segregation of each marker and linkage was analyzed by using JoinMap version 3.0. Mapped markers were aligned in ten linkage groups which covered 887.8 cM with an average marker interval of 4.47 cM. Markers showing skewed segregation ratio were clustered in six LGs.Quantitative trait loci (QTL) were mapped for bolting resistance by using MAPQTL 4.0 package. Four QTLs explaining from 7.0 to 9.4% of the total variation were detected, all of them increase bolting resistance. These mapped QTLs could be used to develop a marker assisted selection programme for bolting resistance breeding.     

小麦蛋白磷酸酶2A结构亚基基因TaPP2Aa的功能标记作图

 【目的】开发小麦抗旱相关蛋白磷酸酶结构亚基基因TaPP2Aa的功能标记并作图,为分子标记辅助选择抗逆育种提供依据。【方法】测序得到普通小麦及其野生近缘种TaPP2Aa的基因序列,分析其SNP位点差异,设计3对基因组特异引物和6对基因组内等位基因特异引物,利用中国春缺四体对TaPP2Aa进行染色体定位,利用RIL群体（Opata 85×W7984）和DH群体（旱选10号×鲁麦14）进行该基因的功能标记作图。【结果】TaPP2Aa定位于小麦第5同源染色体群上;TaPP2Aa-B位于RIL群体5B的标记区间Xwg909—Xgwm67,与2个标记的遗传距离分别为4.0 cM和3.6 cM,在DH群体5B染色体的标记区间Xgwm234—WMC363,与WMC363的遗传距离为7.5 cM;在2个遗传群体中与标记Xgwm67的距离分别为3.6 cM和11.4 cM。TaPP2Aa-D位于RIL群体染色体5D的标记区间Xcmwg770—Xbarc205,遗传距离分别为9.8 cM和10.0 cM。【结论】确定了TaPP2Aa所在的染色体位置,通过与DH和RIL 2个遗传作图群体中已有的抗逆主效QTL进行对比分析,明确了TaPP2Aa与小麦抗逆性状QTL具有遗传连锁关系,开发的功能标记可用于小麦抗逆性状的分子标记辅助选择。     

QTLs for Sugar Content of Stalk in Sweet Sorghum （Sorghum bicolor L.Moench）

High sugar content of sorghum stalk is an important factor in the sorghum silage production. To identify the genomic regions controlling sugar content and to develop molecular markers linked to sugar content in sweet sorghum, we used an F2：3 segregating population consisting of 207 individuals derived from a cross between a high sugar content inbred line, Early Folger, and a normal inbred line, N32B, for genetic linkage mapping and quantitative trait locus （QTL） analysis. We constructed a genetic linkage map spanning 983.5 cM based on a total of 327 markers comprising 31 restriction fragment length polymorphism （RFLP） markers, 254 amplified fragment length polymorphism （AFLP） markers, and 42 simple sequence repeat （SSR） markers. In the 20 linkage groups detected, 98.2% of markers aligned to the 10 linkage groups of sorghum. Variations in sugar content at different growth stages and among internodes suggested that the sugar content of middle internodes is stable and suitable for measuring at early dough stage. The broad sense heritability （hB0 of sugar content was 0.64 and 0.62 estimated from the data of F3 families and each parent in 2003 and 2004. We identified one and two QTLs accounting for 22.2 to 25.0% of phenotypic variance using simple interval mapping method in 2003 and 2004, respectively. These two QTLs showed a negative additive effect, and over-dominance effect. A QTL on LG-D was detected in both two years. Above results will be help us to understand the genetic mechanism of sugar content in sorghum and the QTL detected in this study might be useful in the improvement of sugar content by marker-assisted selection.     

玉米QR-001/QS-001组合F_2群体SSR连锁图谱构建

以自育的高抗玉米粗缩病自交系QR-001为母本、高感自交系QS-001为父本,配制了包含281个单株的F2分离群体为作图群体。选用在玉米基因组中均匀分布的1 028对SSR引物在双亲间进行多态性引物的筛选,共检测到110个可以鉴别F2群体各单株标记基因型的SSR多态性标记。借助QTL IciMapping Version 3.3软件构建了较好覆盖玉米10条染色体的分子标记连锁图谱,图谱总长度为1 343.2 cM,标记间平均距离为10.3 cM。其中1个分子标记(bnlg161)不与连锁群连锁。所建连锁群中有26.6%的SSR分子标记发生偏分离。该图谱的构建为玉米抗粗缩病QTL定位、分子标记辅助选择和分子设计抗病育种等研究奠定了基础。     

鲜食甜玉米南方锈病抗性QTL定位分析

为挖掘新的抗南方锈病基因资源,本研究以甜玉米组合M5×M114的216个F2单株为遗传作图群体,应用BSA方法从500对SSR引物中筛选出2对在F2代抗病和感病DNA池间具有多态性的引物,分别位于4和9号染色体上;在4和9号染色体上重新设计100对SSR引物,构建了包含33个标记位点总长为241.2cM的连锁遗传图,各个标记间的平均距离为7.53cM。结合F2单株对南方锈病的抗性表现,用复合区间作图法在4和9号染色体上共检测到7个显著的南方锈病抗性QTLs,其中:4个QTLs位于4号染色体上,可解释12.1%、7.8%、18.2%和14.9%表型变异;3个位于9号染色体上,分别解释17.0%、13.3%与19.2%的表型变异。研究结果可为抗南方锈病的精细定位、主效基因克隆和抗南方锈病鲜食甜玉米品种选育提供理论依据。     

Molecular Mapping of Two Novel Stripe Rust Resistant Genes YrTp1 and YrTp2 in A-3 Derived from Triticum aestivum × Thinopyrum ponticum

Loss of variety resistance to stripe rust (Puccinia striiformis Westend f. sp.tritici) is an important factor causing massive periodical epidemic of rust in wheat production. Creation and development of new races of rust pathogen have led to serious crisis of resistance loss in widely planted varieties. This has quickened the search for new resistance resources. Molecular marker could facilitate the identification of the location of novel genes. A line A-3 with high resistance (immune) to currently epidemic yellow rust races (CY29, 31, 32) was screened out in offspring of Triticum aestivum × Thinopyrum ponticum. Segregation in F₂ and BC₁ populations indicated that the resistance was controlled by two independent genes: one dominant and one recessive. SSR markers were employed to map the two resistant genes in the F₂ and BC₁ populations. A marker WMC477-_167bp located on 2BS was linked to the dominant gene with genetic distance of 0.4 cM. Another marker WMC364-_{208 bp} located on 7BS was linked to the recessive-resistant gene with genetic distance of 5.8 cM. The two genes identified in this paper might be two novel stripe rust resistant genes, which were temporarily designated as YrTp1 and YrTp2, respectively. The tightly linking markers facilitate transfer of the two resistant genes into the new varieties to control epidemic of yellow rust.     

基于EST-SSR标记甘薯连锁图谱构建及淀粉性状的QTL定位

【目的】利用分子标记技术,构建甘薯遗传连锁图谱,并分析甘薯淀粉含量性状的QTL位点,为高淀粉含量甘薯种质资源利用及甘薯分子标记辅助育种提供理论和实践依据。【方法】以高淀粉含量品种万薯5号为母本、低淀粉含量品种商丘52-7为父本建立杂交群体,利用EST-SSR标记,采用"双假测交"策略和运用Join Map4.0软件,分别构建双亲遗传连锁图谱,并结合F1(2012、2013年)群体表型数据采用区间作图法对淀粉含量性状进行QTL检测。【结果】利用1 679对EST-SSR引物筛选出的1 045对多态性引物检测F1群体的标记基因型,获得了1 418个标记位点。分别对上述获得的父母本多态性标记进行遗传连锁分析,在LOD≥5.0情况下,分别构建父母本的连锁遗传图谱。采用642个标记的多态性位点构建母本连锁群74个,其中,215个标记位点位于连锁图谱上,占标记多态性位点总数的33.5%。每个连锁群上有2—11个标记位点,连锁群长度在0.6—129.4 cM,图谱总长为3 826.07 c M,标记间平均距离为17.80 c M。属于父本的776个标记位点构建了80个连锁群,共有252个标记位点构建在连锁图谱上,占标记总数的32.5%,每个连锁群上有2—24个标记位点,连锁群长度在2.0—156.8 c M,图谱总长为3 955.0 cM,标记间平均距离为15.7 c M。以F1杂交群体构建的遗传连锁图谱,结合2012年、2013年2个环境,利用QTL作图软件MapQTL5.0,采用区间作图法进行分析,共检测到17个与淀粉含量性状相关的QTL,贡献率在8.4%—40.5%。其中qWsc-1、qWsc-2、qWsc-3 3个QTL位于母本万薯5号连锁群上,且在2年环境中均可检测到;14个QTL位于父本商丘52-7连锁群上,qSsc-1、qSsc-2、qSsc-3、qSsc-4、qSsc-8、qSsc-10、qSsc-11、qSsc-12是在2个环境均检测到的QTL。qSsc-5、qSsc-6、qSsc-7、qSsc-9、qSsc-13、qSsc-14是只在1个环境检测到的QTL。标记GDAAS0603在双亲中和2个环境中均同时检测到,这些环境稳定QTL可用于分子标记辅助选择。【结论】分别构建了亲本EST-SSR分子标记连锁群图谱,丰富了构建甘薯图谱的标记类型,定位了17个与淀粉含量相关的QTL位点。     

A Genetic Linkage Map of Kenaf （Hibiscus cannabinus L.） Based on SRAP,ISSR and RAPD Markers

Kenaf (Hibiscus cannabinus L.) is one of the most economically important crops for non-wood fiber production. The objective of this study was to establish a genetic linkage map of kenaf with higher density of molecular markers. A semi-wild variety Ga42 and a cultivar Alain kenaf were used as parents to construct an F₂ population consisting of 155 plants. The genetic linkage map comprising 134 marker loci was constructed, including 65 sequence-related amplified polymorphism (SRAP), 56 inter-simple sequence repeat (ISSR), and 13 randomly amplified polymorphic DNA (RAPD) markers. This map spans 2 108.9 cM and contains 20 linkage groups with an average marker density of 15.7 cM between the adjacent markers.