A microsatellite marker linked to leaf rust resistance transferred from Aegilops triuncialis into hexaploid wheat

Aegilops triuncialis (UUCC) is an excellent source of resistance to various wheat diseases, including leaf rust. Leaf rust‐resistant derivatives from a cross of a highly susceptible Triticum aestivum cv.‘WL711’ as the recurrent parent and Ae. triuncialis Ace.3549 as the donor and with and without a pair of acrocentric chromosomes were used for molecular tagging. The use of a set of sequence tagged microsatellite (STMS) markers already mapped to different wheat chromosomes unequivocally indicated that STMS marker gwm368 of chromosome 4BS was tightly linked to the Ae. triuncialis leaf rust resistance gene transferred to wheat. The presence of the Ae. Triuncialis‐specific STMS gwm368 homoeoallele along with the non‐polymorphic 4BS allele in the rust‐resistant derivatives with and without the acrocentric chromosome indicates that the resistance has been transferred from the acrocentric chromosome to either the A or the D genome of wheat. This alien leaf rust resistance gene has been temporarily named as LrTr.     

Identification and validation of a major QTL for salt tolerance in soybean

To identify quantitative trait loci (QTLs) conditioning salt tolerance in soybean (Glycine max (L.) Merr.), two recombinant inbred line (RIL) populations derived from crosses of FT-Abyara × C01 and Jin dou No. 6 × 0197 were used in this study. The FT-Abyara × C01 population consisted of 96 F₇ RILs, and the Jin dou No. 6 × 0197 population included 81 F₆ RILs. The salt tolerant parents FT-Abyara and Jin dou No. 6 were originally from Brazil and China, respectively. The QTL analysis identified a major salt-tolerant QTL in molecular linkage group N, which accounted for 44.0 and 47.1% of the total variation for salt tolerance, in the two populations. In the FT-Abyara × C01 population, three RILs were found to be heterozygous around the detected QTL region. By selfing the three residual heterozygous lines, three sets of near isogenic lines (NILs) for salt tolerance were developed. An evaluation of salt tolerance of the NILs revealed that all the lines with FT-Abyara chromosome segment at the QTL region showed significantly higher salt tolerance than the lines without the FT-Abyara chromosome segment. Results of the NILs validated the salt tolerance QTL detected in the RIL populations.     

DAF marker tightly linked to a major locus for Ascochyta blight resistance in chickpea (Cicer arietinum L.)

Resistance of chickpea against the disease caused by the ascomycete Ascochyta rabiei is encoded by two or three quantitative trait loci, QTL1, QTL2 and QTL3. A total of 94 recombinant inbred lines developed from a wide cross between a resistant chickpea line and a susceptible accession of Cicer reticulatum, a close relative of cultivated chickpea, was used to identify markers closely linked to QTL1 by DNA amplification fingerprinting in combination with bulked segregant analysis. Of 312 random 10mer oligonucleotides, 3 produced five polymorphic bands between the parents and bulks. Two of them were transferred to the population on which the recent genetic map of chickpea is based, and mapped to linkage group 4. These markers, OPS06-1 and OPS03-1, were linked at LOD-scores above 5 to markers UBC733B and UBC181A flanking the major ascochyta resistance locus. OPS06-1 mapped at the peak of the QTL between markers UBC733B (distance 4.1 cM) and UBC181A (distance 9.6 cM), while OPS03-1 mapped 25.1 cM away from marker UBC733B on the other flank of the resistance locus. STMS markers localised on this linkage group were transferred to the population segregating for ascochyta resistance. Three of these markers were closely linked to QTL1. Twelve of 14 STMS markers could be used in both populations. The order of STMS markers was essentially similar in both populations, with differences in map distances between them. The availability of flanking STMS markers for the major resistance locus QTL1 will help to elucidate the complex resistance against different Ascochyta pathotypes in future. This revised version was published online in August 2006 with corrections to the Cover Date.     

Characterization of near-isogenic lines carrying QTL for high spikelet number with the genetic background of an indica rice variety IR64 (Oryza sativa L.)

Total spikelet number per panicle (TSN) is one of the most important traits associated with rice yield potential. This trait was assessed in a set of 334 chromosomal segment introgression lines (ILs: BC₃-derived lines), developed from new plant type (NPT) varieties as donor parents and having the genetic background of an indica-type rice variety IR64. Among the 334 ILs, five lines which had different donor parents and showed significantly higher TSN than IR64 were used for genetic analysis. Quantitative trait locus (QTL) analysis was conducted using F₂ populations derived from crosses between IR64 and these ILs. As a result, a QTL for high TSN (one from each NPT donor variety) was detected on common region of the long arm of chromosome 4. The effect of the QTL was confirmed by an increase in TSN of five near-isogenic lines (NILs) developed in the present study. The variation in TSN was found among these NILs, attributing to the panicle architecture in the numbers of primary, secondary and tertiary branches. The NILs for TSN and the SSR markers linked to the TSN QTLs are expected to be useful materials for research and breeding to enhance the yield potential of rice varieties.     

玉米衔接式单片段导入系群体的构建和评价

以生产上广泛种植的玉米杂交种豫玉22的亲本自交系87-1和综3为受体亲本,以糯质、抗病性较好的玉米自交系衡白522为供体亲本,采用回交和自交的方法,结合SSR分子标记辅助选择,分别构建了以87-1和综3为背景的衔接式玉米单片段导入系群体,并对其遗传背景、导入片段大小、数目和覆盖率等进行了评价。结果表明,87-1背景的导入系群体导入了40个供体片段,片段长度介于0.03~342.8 cM,平均长度为91.1 cM,导入片段总长为3 643.9 cM,覆盖率为48.9%;综3背景的导入系群体导入了78个供体片段,片段长度介于0.03~343.4 cM,平均长度为75.5 cM,导入片段总长为5 895.2 cM,覆盖率为79.2%。     

以性状和分子标记为基础的水稻近等基因系的分离

以珍汕97/明恢63的一个含234个重组自交系的F6：7群体为材料, 通过以性状和分子标记为基础的方法在该群体中分离了每穗实粒数和千粒重这两个性状的近等基因系及对这两个性状有效应的QTL标记位点和两两互作位点的近等基因系。 在重组自交系RIL65和RIL197家系内分别分离了每穗实粒数和千粒重的近等基因系。 在重组自交系RIL54     

QTL analysis for grain weight in common wheat

Quantitative trait loci (QTL) analysis for grain weight (GW = 1000 grain weight) in common wheat was conducted using a set of 100 recombinant inbred lines (RILs) derived from a cross ‘Rye Selection 111 (high GW) × Chinese Spring (low GW)’. The RILs and their two parental genotypes were evaluated for GW in six different environments (three locations × two years). Genotyping of RILs was carried out using 449 (30 SSRs, 299 AFLP and 120 SAMPL) polymorphic markers. Using the genotyping data of RILs, framework linkage maps were prepared for three chromosomes (1A, 2B, 7A), which were earlier identified by us to carry important/major genes for GW following monosomic analysis. QTL analysis for GW was conducted following genome-wide single marker regression analysis (SMA) and composite interval mapping (CIM) using molecular maps for the three chromosomes. Following SMA, 12 markers showed associations with GW, individual markers explaining 6.57% to 10.76% PV (phenotypic variation) for GW in individual environments. The high grain weight parent, Rye Selection111, which is an agronomically superior genotype, contributed favourable alleles for GW at six of the 12 marker loci identified through SMA. The CIM identified two stable and definitive QTLs, one each on chromosome arms 2BS and 7AS, which were also identified through SMA, and a third suggestive QTL on 1AS. These QTLs explained 9.06% to 19.85% PV for GW in different environments. The QTL for GW on 7AS is co-located with a QTL for heading date suggesting the occurrence of a QTL having a positive pleiotropic effect on the two traits. Some of the markers identified during the present study may prove useful for marker-assisted selection, while breeding for high GW in common wheat.     

RAPD markers linked with restorer genes for the C-source of cytoplasmic male sterility in rye (Secale cereale L.)

The study was aimed at the identification of random amplified polymorphic DNA markers linked to genes controlling male sterility in rye with the C‐source of sterility‐inducing cytoplasm. Markers of male sterility were distinguished using bulk segregant analysis, carried out on the two F₂ crosses between male sterile and male fertile inbred lines. Screening of polymorphisms revealed by 1000 arbitrary 10‐mer primers allowed the detection of 10 markers in the cross between 711‐cmsC and DS2 lines and seven markers in the cross between 544‐cmsC and Ot0‐20 lines. Five markers were common for the two crosses, which allowed comparative mapping to be performed. Ten markers were mapped on the 4RL chromosome arm where two linked quantitative trait loci (QTL) for male sterility were discovered. Additional QTL of minor effect on male fertility were detected between the two linked markers provisionally assigned to the 6RS chromosome arm. The effectiveness of the marker‐assisted selection (MAS) for male‐sterile genotypes was evaluated.     

Evaluation of cold hardiness in two sets of near-isogenic lines of wheat (Triticum aestivum) with polymorphic vernalization alleles

In wheat, variation at the orthologus Vrn‐1 loci, located on each of the three genomes, A, B and D, is responsible for vernalization response. A dominant Vrn‐1a allele on any of the three wheat genomes results in spring habit and the presence of recessive Vrn‐1b alleles on all three genomes results in winter habit. Two sets of near‐isogenic lines (NILs) were evaluated for DNA polymorphisms at their Vrn‐A1, B1 and D1 loci and for cold hardiness. Two winter wheat cultivars, ‘Daws’ and ‘Wanser’ were used as recurrent parents and ‘Triple Dirk’ NILs were used as donor parents for orthologous Vrn‐1 alleles. The NILs were analysed using molecular markers specific for each allele. Only 26 of 32 ‘Daws’ NILs and 23 of 32 ‘Wanser’ NILs had a plant growth habit that corresponded to the marker genotype for the markers used. Freezing tests were conducted in growth chambers programmed to cool to ?21.5°C. Relative area under the death progress curve (AUDPC), with a maximum value of 100 was used as a measure of death due to freezing. The average relative AUDPC of the spring habit ‘Daws’Vrn‐A1a NILs was 86.15; significantly greater than the corresponding winter habit ‘Daws’Vrn‐A1b NILs (42.98). In contrast, all the ‘Daws’Vrn‐A1bVrn‐B1aVrn‐D1b and Vrn‐A1bVrn‐B1bVrn‐D1a NILs (spring habit) had relative AUDPC values equal to those of their ‘Daws’ sister genotypes with Vrn‐A1bVrn‐B1bVrn‐D1b NILs (winter habit). The average AUDPC of spring and winter habit ‘Wanser’ NILs differed at all three Vrn‐A1, Vrn‐B1 and Vrn‐D1 locus comparisons. We conclude that ‘Daws’ and ‘Wanser’ have different background genetic interactions with the Vrn‐1 loci influencing cold hardiness. The marker for Vrn‐A1 is diagnostic for growth habit and cold hardiness but there is no relationship between the Vrn‐B1 and Vrn‐D1 markers and the cold tolerance of the NILs used in this study.     

利用品质性状的回交选择导入系挖掘水稻抗纹枯病QTL

将优质、抗纹枯病的高秆供体Tarom Molaii和Binam导入半矮秆IR64和特青背景,培育品质性状回交选择构建的4个导入系群体IR64/Tarom Molaii、特青/Tarom Molaii、IR64/Binam和特青/Binam,定位了影响水稻抗纹枯病病级(disease scale, DS)、相对病斑高度(relative lesion height, RH)和株高(plant height, PH)的QTL。结果表明,4个导入系群体的DS与RH高度相关,两者与PH呈显著负相关。导入系后代各性状均呈现超亲分离,出现抗性明显优于双亲的抗病个体,其中40%左右属半矮秆抗病类型。采用单向方差分析,在这4个群体中分别定位到10、8、8和6个影响3个性状的QTL,多数基因座上降低DS和RH即增强抗病性同时增加株高的等位基因均来自两个供体。未在同一供体两个不同背景下检测到影响3个性状的相同QTL,表明抗纹枯病QTL表达有明显的遗传背景效应。PH与DS及PH与RH被定位在同一个显著标记位点的QTL数分别占两个性状QTL总数的38%和52%,表明水稻纹枯病抗性与株高关系密切,两者存在许多连锁位点。与以往相同群体品质性状QTL的定位结果相比,发现品质性状QTL与抗纹枯病QTL大多分布在染色体的不同区域,彼此独立遗传。对利用目标性状选择导入系定位非目标性状QTL的效果、影响因素及育种应用进行了探讨,强调了目标性状选择导入系对非目标性状QTL发掘及育种应用的重要性。     

Identification of novel QTL for leaf traits in soybean

Several leaf traits of soybean (Glycine max L. Merr.), including leaf area (LA), leaf shape (LS) and specific leaf weight (SLW) may be related to soybean yield. The objective of this study was to identify novel quantitative trait loci (QTL) for LA, LS and SLW in a recombinant inbred line (RIL) population. The phenotype data were collected in 2011 and 2012 for 93 F_7:10 RILs using a randomized complete block design with 2 replicates each year. Five hundred and sixteen single‐nucleotide polymorphism (SNP) markers and the phenotype data were used to detect QTL using single marker analysis (SMA) and composite interval mapping (CIM). Single markers analysis identified 26 QTL for the three traits, of which 17 were novel and the rests were previously reported QTL. Most of these QTL were also identified by CIM. Most QTL reported in this study were in close proximity (<1 cM) of one or more SNP markers. These publicly available SNP markers with close linkage to LA, LS and SLW should be useful for marker‐assisted breeding for these traits.     

Identification of quantitative trait loci for seed isoflavone concentration in soybean (Glycine max) against soybean cyst nematode stress

Isoflavones are plant secondary metabolites produced in soybean (Glycine max), which provide plant defense against pathogens and are beneficial to human health. Soybean cyst nematode (SCN) is a major yield‐limiting pest in most soybean‐producing area across the world. Traits, seed isoflavones and SCN resistance are quantitative in nature, and their phenotypic evaluations are expensive. Quantitative trait loci (QTL) underlying the two traits will be helpful to develop SCN‐resistant lines with elevated isoflavones using marker‐assisted‐selection (MAS). This study aims to identify isoflavones and SCN‐related QTL in a soybean population consisting of 109 RILs, which was developed from a cross between two commercial soybean cultivars viz. ‘RCAT1004’ and ‘DH4202’ and grown in four non‐SCN and SCN‐infested fields during 2015 and 2016. While single marker ANOVA identified 10 QTL for isoflavones and five for SCN (p < 0.01), simple interval and multiple QTL mappings identified four QTL associated with isoflavones (LOD ≥ 2.2). These results contribute to a better understanding of the genetics of the two traits and provide molecular markers that can be used in MAS to facilitate developing SCN‐resistant soybeans with increased isoflavones.     

A comparison of marker-assisted and phenotypic selection for high grain protein content in spring wheat

Wheat grain protein content (GPC) is a primary end-use quality determinant for hard spring wheat (Triticum aestivum L.), and marker-assisted selection (MAS) could help plant breeders to develop high GPC cultivars. Two experiments were conducted using two populations developed by crossing low GPC cultivars (Ember) and (McVey) with (Glupro), which contains a high GPC QTL from Triticum dicoccoides (DIC). In one experiment, MAS and phenotypic selection (PS) were employed to select high GPC genotypes, and the selected genotypes were grown in six North Dakota (ND), USA environments. In a second experiment, molecular markers were used to select BC₂F₂ plants from each marker class for the DIC allele from each population. These plants were twice self-pollinated to produce BC₂F₄ plants, which were grown in single ND and Minnesota (MN) environments. Mean GPC was highest among lines using PS at two environments and not significantly different between MAS and PS in the other four environments. Lines presumably homozygous for DIC alleles had significantly higher GPC than their respective low GPC parents. The phenotypic GPC variation explained by the markers (r ²) was 30% at the ND and 15% at the MN environment. The use of PS was as effective as MAS in selecting for high GPC genotypes and more effective in some environments. This likely can be attributed to PS enabling selection for both the major QTL and other genes contributing to GPC. The use of molecular markers might be more advantageous for transferring the high GPC DIC QTL in a backcrossing program during parent development.     

水稻RFLP连锁图谱的构建及控制小穗不育和花粉不育的QTL分析

用台中65(粳稻)/ARC10313(籼稻)的重组近交系(F10)构建了RFLP连锁图谱, 含113个分布均匀的标记. 作成的图谱覆盖全基因组, 全图总长1462.4 cM, 图中标记位置与所使用的参照图谱基本符合. 利用该重组自交家系材料与亲本台中65回交得到BF1家系, 用于对小穗不育和花粉不育的QTL分析, 检测出3个小穗不育和1个花粉不育QTL, 且有一     

基于性状和分子标记的小麦抗旱近等基因系的分离

创建小麦‘宁春4号’抗旱近等基因系,为其在生产中的应用和抗旱遗传改良提供有利用价值的材料。利用重组自交系(RILs)合适世代(F₆或F₇)的单株具有一定杂合率的特点,采用性状和分子标记分离近等基因系的方法,在‘宁春4号’/‘宁春27号’RILs一个家系RIL-97内分离出‘宁春4号’抗旱近等基因系,经抗旱性及特征特性鉴定表明,该近等基因系抗旱性较强,其他形态特征特性与‘宁春4号’基本一致。这些近等基因系可进一步用来精确定位抗旱相关性状QTL位点。利用RILs群体合适世代结合分子标记是快速构建近等基因系的有效方法。     

Detection of quantitative trait locus for leaffolder (Cnaphalocrocis medinalis (Guenée)) resistance in rice on linkage group 1 based on damage score and flag leaf width

Rice leaffolder (RLF) (Cnaphalocrocis medinalis (Guenée) is a destructive and widespread insect pest throughout the rice growing regions in Asia. The genetics of resistance to RLF in rice is very complex and not thoroughly explored. The present study was conducted to detect the quantitative trait loci (QTL) associated with RLF resistance involving 176 recombinant inbred lines (RILs) of F₈ generation derived from a cross between IR36, a leaffolder susceptible variety and TNAULFR831311, a moderately resistant indica rice culture. Simple sequence repeat (SSR) markers were used to construct specific linkage groups of rice. All the RILs were screened to assess their level of resistance to RLF by measuring the leaf area damaged. Besides this, the length and width of the flag leaf of each RIL were measured since these two parameters were considered as correlated traits to the RLF resistance in rice. All the above parameters observed across the RILs showed quantitative variation. Correlation analysis revealed that damage score based on greenhouse screening was positively correlated with length and width of the flag leaf. Out of 364 SSR markers analysed, 90 were polymorphic between the parents. Multi-point analysis carried out on segregating 69 SSR marker loci linkage group wise resulted in construction of linkage map with eleven groups of 42 SSR markers. Through single marker analysis, 19 SSR markers were found to have putative association with the three phenotypic traits studied. Of these markers, RM472 was identified as a locus having major effect on RLF resistance trait based on length of the flag leaf. Interval mapping detected two QTLs on linkage group 1. Among these QTLs, the QTL flanked by RM576–RM3412 were found to be associated with width of the flag leaf and RLF resistance. The putative SSR markers associated with leaffolder resistance identified in the present study may be one of the loci contributing resistance to RLF in rice.     

利用重组自交群体检测水稻抗亚铁毒胁迫的QTLs

潜育性水稻田广泛分布于中国、斯里兰卡、印度、印度尼西亚、塞拉里昂、利比亚、尼日利亚、哥伦比亚和菲律宾等国，其中我国南方稻区就有670万公顷低产潜育性水稻田。该类水稻田还原性强，矿质营养失调，尤以Fe2+ 过量积累，对水稻生长发育产生不良的逆境胁迫作用。培育抗亚铁毒的水稻品种是简便、经济有效地提高稻谷产量的重     

Genome mapping and molecular markers identification for yield,yield component and fibre quality traits in tetraploid cotton

The identification of quantitative trait loci (QTL) across different environments is a prerequisite for marker‐assisted selection (MAS) in crop improvement programmes. CottonSNP63k Illumina infinium array was used for genotyping 178 inter‐specific recombinant inbred lines and the parents, and identified 1,667 homozygous polymorphic markers between the parents. Of these, 1,430 markers were used for the construction of linkage map after removing 237 redundant markers. The genetic map spans a total genetic length of 3,149.8 cM with an average marker interval size of 2.2 cM. The phenotypic data from five environments were analysed separately using inclusive composite interval mapping which identified a total of 56 QTL explaining phenotypic variances (PVE) in the range of 8.18%–28.91%. There were 11 and 24 major QTL found for fibre quality and yield components, respectively. A total of 64 QTL were identified through Multi‐Environment Trials analysis, of which 34 recorded QTL × Environment interactions.     

Bayesian QTL mapping for recombinant inbred lines derived from a four-way cross

Recombinant inbred lines (RILs) are created by a cross between inbred lines followed by repeated selfing or sib-mating, which include many different types of new inbred lines with many recombination events on the genome. The phenotype of each RIL can be assessed based on multiple individuals within the same line to reduce non-genetic variability. Therefore, RILs are useful tools for QTL mapping allowing effective detection and fine localization of QTL. Usually only two inbred lines are involved to create RILs. In such two-way RILs, however, there are at most two different alleles at QTL and only QTL segregating between two parental lines can be detected. Recently a new crossing design using multiple founders for creating RILs was proposed in Arabidopsis thaliana and mice, where the genome of each RIL is a mosaic of the genomes from multiple parents. Such multi-way RILs are more useful to improve the efficiency in QTL detection than two-way RILs because of the increased chance of QTL segregation among multiple lines, leading to the successful detection of many QTL. In this paper, we propose a Bayesian method for mapping multiple QTL simultaneously in four-way RILs allowing the inference about the equivalence relationship among the four possible alleles descended from the four founder lines as well as the estimation of QTL locations and effects via a MCMC algorithm. Simulation experiments show that our method has the practical ability to detect QTL and to provide the information of equivalence relationship among alleles at detected QTL using four-way RILs.