Genetic analysis and QTL mapping of growth period traits and plant height traits in soybean recombinant inbred lines from Dongnong 47 × PI 317334-B

High and stable yield is the main goal of soybean genetic improvement. In this study, association analysis was used to detect the quantitative trait loci (QTL) for the plant height, and soybean growth period using 182 SSR markers in the RIL population of 136 F_4:8 lines, which developed from a cross between photoperiod-insensitive cultivar ‘Dongnong 47’ and photoperiod-sensitive variety PI317334–B. The results showed that 33 QTLs related to soybean growth period and plant height traits were detected by compound interval mapping, and were located on 12 linkage groups including N, C1, C2, J, D1a, B2, E, G, A2, O, L, I, with the contribution rate of 7.85–33.84%. These QTL loci and linkage markers related to soybean photoperiod sensitivity, would be helpful to identify key genes that control soybean photoperiod sensitivity, and provide an important basis for the breeding of new photoperiod-insensitive soybean varieties based on molecular design breeding.     

Mapping QTL of Fiber Yield and Quality Traits in F2 Populations of Chromosome Segment Substitution Lines from Gossypium hirsutum × Gossypium barbadense

In this study, F₂ populations from two chromosome segment substitution lines MBI7455 and MBI7358, were quantified using SSR to evaluate the parents' genotype and detect QTL related to fiber quality plus yield traits of cotton. Results show that the recurrent parent (CCRI45) hosted 96.70% and 95.60% of chromosome segment substitution in MBI7455 with 12 chromosome segments and in MBI7358 with 16 chromosome substitution segments of Gossypium barbadense, respectively. In the F₂ population, the average rate of chromosome substitution of the recurrent parent (CCRI45) was 96.44%, and the average segments of chromosome substitution of Gossypium barbadense was 13.42, with an average segments of homozygous donor chromosome value of 3.90. Analysis showed 19 fiber quality-related QTL with a phenotypic variance of between 2.52%-13.11% and seven yield traits-related QTL with a range of 2.93%-11.40% phenotypic variance, resulting in a total of 26 QTL. The CSSLs could be used to detect QTL for fiber yield and quality traits, which offer an important foundation for the cotton molecular-assisted breeding.     

玉米粒重一致性QTL整合图谱的构建及元分析

为进一步研究候选基因发掘、克隆以及基因组结构,在生物信息学基础上,利用公共网络资源上已发表的149个玉米粒重相关QTL位点信息,初步探讨了玉米粒重"一致性"QTL发掘。结果表明:构建出一个包含了80个玉米粒重QTL位点的整合图谱,并在第7染色体上确定出一个"一致性"QTL,由标记bcd349和gpm760a界定,置信区间为463.29~505.50,间距42.21cM。     

杜洛克与二花脸杂交猪群体SNP偏分离分析

偏分离（TRD）是生物中普遍存在的现象,本研究拟在高密度基因芯片判断基因型的大规模群体中挖掘猪基因组标记位点的偏分离位点并探究其潜在的遗传机制。本研究用60K Illumina Porcine SNP芯片对1 020头F2资源家系（杜洛克与二花脸杂交F0-F2群体）进行基因型分型,用偏分离分析软件TRDscan （BF>100）和TDT （P<0.01）方法在单个位点上检测偏分离信号,并对二者共有的显著信号位点附近100 kb窗口的基因进行功能分析。此外,本研究还利用单倍型分型的软件包PHASEBOOK采用多位点连锁分析的策略分析了父源和母源配子中的偏分离区域,并在该区域内搜寻潜在的QTLs。结果表明：1）在单位点的偏分离分析中共鉴定到44个显著的偏分离位点,筛选到23个相关基因;对父本和母本特异性偏分离效应进行分析时,分别鉴定到27和35个显著偏分离位点,其中,分别有11和25个位点的100 kb附近有已注释的功能基因。2）基于单倍型多位点连锁的偏分离结果显示,父本显著偏分离位点位于5和13号染色体上,在该偏分离区域内搜寻功能相关的QTL,共搜寻到3个与繁殖性状（木乃伊数、产活仔数、黄体数）有关的QTLs;分析母本偏分离位点时,在4、6和12号染色体上定位到显著偏分离区域,结合已知的猪QTL数据库,共找到了5个与繁殖性状相关的QTLs。本研究利用大规模猪家系数据系统地鉴别了猪基因组的偏分离位点,为解析猪中的偏分离现象和进一步探究其生物学机制提供了一定的参考作用。     

不同水分环境下玉米叶面积QTL定位及候选基因分析

玉米叶面积的大小及分布特征不仅影响其光合效率、蒸腾速率,而且与其耐旱性、耐密性、抗倒伏性及产量形成紧密相关。深入剖析不同水旱环境下玉米不同生育时期不同叶位叶面积的分子遗传机理对玉米耐旱高产新品种的选育具有重要意义。本研究以构建的2套F_2∶3群体为试材,在8种水分环境下,采用复合区间作图法（CIM）和基于混合线性模型的复合区间作图法（MCIM）对玉米相应叶（V₁₈时期第10片叶、R₁时期穗三叶）叶面积进行单环境和多环境联合QTL分析;参考玉米基因组B73 RefGen_v3挖掘稳定表达的QTLs （sQTLs）区间内的候选基因,并对其进行功能分析。结果表明,采用CIM法,单环境下2个生育时期2套F_2∶3群体间总共定位到了7个玉米相应叶叶面积QTLs,主要受显性（81.0%）、部分显性（14.3%）和超显性（4.7%）等遗传效应的调控,其中在干旱环境下定位到了5个QTLs。采用MCIM法,在2套F_2∶3群体间总共检测到6个相应叶叶面积的联合QTLs,其中1个表现为显著的QTL与环境的互作（QTL×E, Bin 2.08~2.09）,1对QTLs （Bin 1.08~1.10与 Bin 2.08~2.09）参与了显著的加性与加性（AA）上位性互作。结合CIM和MCIM法进一步分析在2套F_2∶3群体间检测到了6个sQTLs,其分别位于Bin 1.08~1.10、Bin 2.08~2.09、Bin 4.08~4.09、Bin 6.05、Bin 8.03和Bin 10.03处,并在这些sQTLs区间内确定了12个玉米叶发育相关候选基因。采用生物信息学,总共收集了75个玉米叶发育相关候选基因,通过系统进化树分析表明,这些候选基因划分为3大进化分支,且上述检测到的12个候选基因分布于这3大进化分支上。这些结果为系统地解析玉米不同生育时期不同水旱环境下相应叶叶面积的分子遗传机理提供理论依据,检测到的sQTLs可作为叶面积改良的重要染色体区段,检测到的候选基因为其进一步克隆、功能分析及育种应用提供了信息参考。     

Improving Drought Tolerance of Rice by Designed QTL Pyramiding

Drought is the most important factor limiting rice yields in the rainfed areas of Asia. To overcome the problem, we developed a new strategy ＇designed QTL pyramiding＇ to more efficiently develop drought tolerant （DT） rice cultivars. In the first phase of this strategy, we developed large numbers of introgression lines （ILs） in elite backgrounds using backcross （BC） breeding, each of which carries multiple genomic segments for improved DT from a known donor. Then, we genotyped all ILs with SSR markers to track the genomewide pattern of introgression in the DT ILs of 16 BC populations derived from crosses between 2 recipients （IR64 and Teqing） and four different donors. X^2 tests and linkage disequilibrium analyses of introgression in the DT ILs revealed significant frequency shifts at many loci across the genome and non-random associations at the multilocus level as a result of selection for DT in the ILs, which led us to the discovery of putative genetic networks underlying DT in the ILs. The networks each containing all DT loci detected in ILs from a BC population showed some interesting features.     

Mapping QTLs for Yield Stability in Durum Wheat Grown under Different Water Regimes

Among the most important Mediterranean annual crops, durum wheat is widely grown in drought-prone areas. Therefore, improving water-use efficiency （WUE） of durum wheat represents a major breeding goal. IDu-WUE （Improving Durum wheat for Water Use Efficiency and yield stability through physiological and molecular approaches） is a collaborative project among public and private research centres in Italy, Spain and WANA （West Asia and North Africa） countries （Morocco, Tunisia, Syria and Lebanon） funded by the European Union aimed at investigating the genetic variation for WUE and yield stability in durum wheat grown in Mediterranean droughtprone areas. During the first year of the project, a number of morpho-physiological traits （e.g. early vigour, flowering time, leaf rolling, number of fertile tillers, etc.）, WUE, WUE-related traits （e.g. carbon isotope discrimination, canopy temperature, chlorophyll fluorescence, etc.）, yield and its components have been investigated in a RIL population （249 lines） and a collection of ca. 190 durum wheat accessions characterized by a high level of linkage disequilibrium （Maccaferri et al., 2005）,     

大粒型水稻材料粒型性状的QTL定位

研究大粒型水稻材料对粒型相关基因的挖掘具有重要作用,同时也能为水稻超高产育种提供优质的种质资源。本研究以大粒型水稻材料lg1与9311杂交衍生的F2遗传分离群体为对象,分别采用2014年、2015年的粒型数据和2年的联合粒型数据,对控制其粒长、粒宽及粒厚的QTL进行初步定位。结果表明,3种情况下共定位到22个相关QTL,其中5个粒长QTL、9个粒宽QTL、8个粒厚QTL,分布于第1、第2、第3、第4、第5、第8和第11号染色体上。3种情况下均检测到QTL的有3个,即粒长QTL q GL-2-1、粒宽QTL q GW-5-1和粒厚QTL q GT-5-1,3个QTL增效等位基因均来自于亲本lg1;此外,有7个QTL在2014年、2015年和2年的联合数据定位中均被检测到,12个QTL只在1年或2年的联合数据定位中被检测到。q GL-2-1、q GW-2-3和q GT-2-3处于同一标记区间RM5812~RM13174,推测可能受同一粒型基因控制,是新的粒型QTL位点。主效QTL q GL-1-2和q GW-11-1可能是新的控制粒型QTL位点,其余检测到的QTL所在的大部分标记区间已有粒型QTL被定位或克隆。本研究结果为大粒水稻lg1粒型基因的精细定位及克隆奠定了基础。     

利用复合杂交群体定位陆地棉产量性状QTL

以共同亲本渝棉1号分别与中棉所35和贝尔斯诺杂交F1代,再次杂交得到复合杂交群体.利用6 565对SSR引物对3亲本进行多态性引物筛选,获得92对多态性引物.以多态性引物检测复合杂交群体172个单株的标记基因型,共获得96个标记位点,其中4对引物产生两个位点.构建的遗传连锁图谱包括63个标记、19个连锁群,总长656.0 cM,标记问平均距离10.4 cM,覆盖棉花基因组14.8%.利用多QTL作图方法,以复合杂交群体F2株系的产量性状鉴定结果,检测到7个产量性状QTL,即1个单株铃数(BN)、2个单铃重(BW)、1个衣分(LP)、1个单株籽棉(SC)和2个单株皮棉(LC).7个QTL分布于4条D基因组染色体,其中第19染色体分布4个QTL.同时,不同亲本之间存在产量性状QTL等位基因的差异.