Haplotype structure around the nud locus in barley and its association with resistance to leaf stripe (Pyrenophora graminea)

The naked/hulled kernel trait is controlled in barley by a single gene called nud, on chromosome 7H. The first aim of this work was use bulked segregant analysis to find, new PCR‐based markers linked to nud for marker‐assisted selection (MAS). A new SCAR marker (sJ14) was developed, which is useful for introgressing the naked trait. This, and three other SCARs, were placed on the ‘Proctor’ × ‘Nudinka’ map to detail a 0.9‐cM fragment tagging nud. In order to evaluate the haplotypes around the nud locus, a phenotypically differentiated collection of naked/hulled genotypes was characterized by means of the above markers. Eight different marker haplotypes were found in the breeding germplasm, and a new allele for the marker sKT7 was found. The same barley collection has been surveyed for resistance/susceptibility to leaf stripe (Pyrenophora graminea), in order to investigate any possible association between this and other traits. The naked/hulled seed trait was not associated with resistance/susceptibility to the fungus.     

Short Communication Comparison between QTL analysis of powdery mildew resistance in barley based on detached primary leaves and on field data

A quantitative trait loci (QTL) analysis of quantitative powdery mildew resistance was performed on 216 doubled haploid lines derived from a cross between the winter-barley varieties ‘Igri’ and ‘Danilo’ using 67 RFLP loci. Resistance to powdery mildew was determined in the field with natural infection and on detached primary leaves with a specific isolate. The major QTL found in both sets of analysis mapped to the same chromosomal region. No further QTL could be found in the analysis based on detached leaves and one additional minor QTL was found in the analysis based on field data.     

Soybean plant height QTL mapping and meta‐analysis for mining candidate genes

Plant height is closely related to seed yield of soybean. The goal of this study was to identify important loci affecting soybean plant height using meta‐analysis based on a reference physical map. Plant height related to QTLs was mapped across eight years with a RIL population by WinQTLCart v2.5. 182 QTLs related to plant height of soybean from database and our research were collected, and each QTL was projected onto the soybean physical map by software BioMercator v2.1. The confidence interval of meta‐QTL ranged from 0.09 to 5.07 Mb, and the mean phenotypic variance ranged from 4.9% to 73.0%. Furthermore, 4,259 candidate genes were located in these consensus QTLs, and 40 of them were involved in the plant growth and stem elongation and annotated as plant hormone signal transduction (pathway ID ko04075) in KEGG pathway. These results would lay a foundation for fine mapping of QTLs/genes related to plant height and marker‐assisted selection for breeding in soybean.     

Use of component analysis in QTL mapping of complex crop traits: a case study on yield in barley

Genes contributing to the quantitative variation of a complex crop trait can be numerous. However, using existing approaches, the number of quantitative trait loci (QTL) detected for a trait is limited. Therefore, rather than looking for QTL for a complex trait itself, determining QTL for underlying component traits might give more information. In this study the potential of component analysis in QTL mapping of complex traits was examined using grain yield in spring barley as an example. Grain yield was divided into three components: number of spikes/m², number of kernels/spike, and 1000‐kernel weight. These traits were measured for individuals of a recombinant inbred‐line population in field trials conducted over 2 years. By the use of an approximate multiple QTL model, one to eight QTL were detected for each trait in a year. Some QTL were mapped to similar positions in both years. Almost all QTL for yield were found at the position of or in close proximity to QTL for its component traits. A number of QTL for component traits were not detected when yield itself was subjected to QTL analysis. However, relative to the QTL for yield itself, all component‐trait QTL did not explain the variation in yield better. The results in relation to the potential of using component analysis in studying complex crop traits are discussed.     

Effects of loci determining photoperiod sensitivity (Ppd-H1) and vernalization response (Sh2) on agronomic traits in the 'Dicktoo'×'Morex' barley mapping population

The objectives of this research were to determine the individual and interaction effects of the Ppd-H1 and Sh2 loci on agronomic traits under short- and long-photoperiod regimes. Nineteen doubled haploid (DH) lines from the ‘Dicktoo’בMorex’ mapping population, which represented the four genotypes at the Ppd-H1 and Sh2 loci, were pheno-typed in controlled environment photoperiods. Both Ppd-H1 and Sh2 had significant effects on several agronomic traits, in addition to their role in determining first node appearance and flowering time. The magnitude of these effects depended on daylight. Under long-day conditions (18 h) Ppd-H1, and under short-day conditions (12 h) Sh2 was a significant determinant of most characters. The interactions between these two loci were significant for several characters, particularly for yield components, under both long- and short-photoperiod regimes. Under the long-day treatment, Ppd-H1 influenced plant height through the determination of node number. There was an epistatic association between the two loci for both 1000-kernel weight and tillering. The combination of photoperiod insensitivity and vernalization requirement caused a significant increase in tillering. This was paralleled by a decrease in 1000-kernel weight. Under the long-day treatment, neither Ppd-H1 nor Sh2 influenced plant yield. Under short-day conditions, the combination of photoperiod insensitivity and vernalization requirement had a pronounced negative effect on plant yield.     

A novel barley scald resistance gene: genetic mapping of the Rrs15 scald resistance gene derived from wild barley, Hordeum vulgare ssp. spontaneum

Most genes for resistance to barley leaf scald map either to the Rrs1 locus on the long arm of chromosome 3H, or the Rrs2 locus on the short arm of chromosome 7H. Other loci containing scald resistance genes have previously been identified using lines derived from wild barley, Hordeum vulgare ssp. spontaneum. A single dominant gene conditioning resistance to scald was identified in a third backcross (BC3F3) line derived from an Israeli accession of wild barley. The resistance gene is linked to three microsatellite markers that map to the long arm of chromosome 7H; the closest of these loci, HVM49, maps 11.5 cM from the resistance gene. As no other scald resistance genes have been mapped to this chromosome arm, it is considered to be a novel scald resistance locus. As the Acp2 isozyme locus is linked to this scald resistance locus, at 17.7 cM, Acp2 is assigned to chromosome 7H. Molecular markers linked to the novel scald resistance gene, designated Rrs15, can be used in breeding for scald resistance.     

Localization of a resistance gene and identification of sources of resistance to barley leaf stripe

In order to determine more precisely the location of the barley leaf stripe gene, called the ‘Vada-resistance gene’, on barley chromosome 2, 63 chromosome-doubled barley lines were tested. Using data on known chromosome 2 genetic markers, the ‘Vada-resistance gene’ was estimated to be located between the markers MSU21 and Xris45b, and at a distance of about 20% recombination from the powdery mildew resistance gene MILa. We suggest that the ‘Vada-resistance gene’ is designated Rdg1a and that all former leaf stripe resistance gene designations should be rejected. To identify possible new sources of resistance, 11 barley cultivars/lines known to possess leaf stripe resistance and originating from different parts of the world, were tested with one Danish and two Syrian isolates of the leaf stripe fungus. Three apparently genetically different sources of race-specific resistance were found. The ‘Vada-resistance’ in the cultivar ‘Golf was effective against seven out of eight isolates’ populations of the leaf stripe fungus differing in geographical origin.     

甘蓝型油菜早熟性状QTL定位及候选基因筛选

目前对于油菜早熟的研究主要围绕开花期性状进行,虽然开花期与生育期呈显著正相关,但却并不完全一致。对于油菜开花后一系列生长发育进程相关性状的遗传研究和QTL定位鲜有报道。本研究以成熟期差异较大的2个油菜品种‘花前早’和‘Global’构建的DH群体为材料,对影响油菜全生育期的各个发育阶段(开花期、花期持续时间、角果期持续时间和全生育期等)进行表型调查和QTL定位分析。共检测到30个早熟相关性状QTL位点,其中开花期、花期持续时间、角果期持续时间和全生育期等分别检测到12、5、4和9个QTL位点,解释了5.8%~22.4%的表型方差。发现4、2和1个全生育期QTL置信区间分别与开花期、花期持续时间、角果期持续时间位点置信区间完全或部分重叠。筛选到29个可能与油菜早熟性状相关的候选基因,它们通过调控花期或籽粒发育等生长发育进程影响油菜早熟。因此,在早熟性状的研究中,可以同时从开花期和籽粒发育过程入手,不但有利于使熟期进一步提前,也可减缓早熟油菜品种过早开花导致的冬前低温寒潮天气的不利影响。     

Identification and mapping of a QTL for rachis internode length associated with cleistogamy in barley

General knowledge of the closed flowering trait, or cleistogamy, of barley is still limited. The relationship between cleistogamy and spike morphology characters was studied and linkage of cleistogamy genes with a highly significant quantitative trait locus (QTL) for rachis internode length on the long arm of chromosome 2H was detected. The mapping populations consisted of 129 doubled haploid lines of ‘Mikamo Golden’ × ‘Harrington’ and 150 F₂ plants of ‘Misato Golden’ × ‘Satsuki Nijo’. The phenotypic variance explained by this QTL accounted for 77.5% and 82.6% of the variance in rachis internode lengt, respectively, in these two populations. The peaks of the QTL coincided with the positions of the cleistogamy gene loci.     

Genetic mapping of the barley Rrs14 scald resistance gene with RFLP, isozyme and seed storage protein markers

The scald susceptible barley cultivar ‘Clipper’ and a third‐backcross (BC₃) line homozygous for the Rrs14 scald resistance gene that originally came from Hordeum vulgare ssp. spontaneum were grown in replicated field trials. The level of resistance that Rrs14 confers against field populations of the pathogen Rhynchosporium secalis, the causal agent of scald disease, was evaluated. The Rrs14 BC₃ line exhibited 80% and 88% less leaf damage than ‘Clipper’ in 1995 and 1996, respectively. Given this effectiveness of Rrs14, research was undertaken to identify a linked marker locus suitable for indirect selection of Rrs14. Based on linkage to a set of previously mapped loci, Rrs14 was positioned to barley chromosome 1H between the seed storage protein (hordein) loci Hor1 and Hor2, approximately 1.8 cM from the latter locus. The Hor2 locus is thus an ideal codominant molecular marker for Rrs14. The tight linkage between Rrs14 and Hor2 and the availability of alternative biochemical and molecular techniques for scoring Hor2 genotypes, permits simple indirect selection of Rrs14 in barley scald resistance breeding programmes.     

玉米耐深播主效QTL qMES20-10的精细定位及差异表达基因分析

干旱是影响玉米(ZeamaysL.)产量最主要的环境因素之一,具有耐深播特性的玉米种质材料能够吸收土壤深层水分,具有较强的耐旱性,因此研究玉米耐深播性状的遗传机制具有重要的理论和应用价值。本实验室前期已利用耐深播玉米自交系3681-4与普通自交系X178构建的F_2:3群体,在玉米10号染色体上定位到了一个耐深播主效QTLqMES20-10。本研究在此基础上,以X178为轮回亲本,结合前景选择和背景选择,构建了BC₃F_3:4家系,对qMES20-10迚行了确证;幵迚一步利用分子标记辅助选择构建了高代回交群体,将其精细定位于133.3～136.0Mb的区间之内。同时,利用从BC₃F_3:4家系中筛选出的两个近等基因系,迚行差异表达基因分析,发现差异表达基因主要参与了化学性应激反应、氧化还原反应和对氧化胁迫的应激反应。本研究结果为迚一步兊隆耐深播主效QTL qMES20-10奠定了基础。     

Use of recombinant substitution lines for gene mapping and QTL analysis of bread making quality in wheat

Three populations of 41 to 74 homozygous recombinant substitutionlines (RSLs) were used for RFLP mapping and quantitative trait analysis ofthe following parameters: total proteins (%prot), SDS-sedimentationvolume (SDSsed), bread mixing time (Bmxt) and loaf volume (Blvol). TheRSLs were developed from crosses between disomic substitution linesinvolving chromosomes 1A, 1B, and 1D of the high-quality wheat cv.`Cheyenne' (Cnn) substituted into the genetic background of the poorquality cv. `Chinese Spring' (CS). The QTL analysis indicated regions in thethree chromosomes responsible for the differences between CS and thethree disomic substitution lines. The major effect detected on chromosome1A of Cnn was high SDSsed, Bmxt and Blvol associated with the H-M-WGlutenin subunit locus Glu-A1. In addition a QTL was identifieddistally on the long arm of chromosome 1A for Bmxt and Blvol. Ahigh %prot QTL was mapped on the long arm of chromosome 1B of CSand a high Bmxt QTL was mapped on the long arm of chromosome 1B ofCnn. Additionally, this chromosome enhanced SDSsed, Bmxt and Blvol,which were associated with the region of the gliadin and L-M-W Gluteninsubunit locus Gli-B1/Glu-B3. A second more proximal region on theshort arm of chromosome 1B could be involved in loaf volume. QTLanalyses for% prot, showed a strong clear QTL mapped in the centromericregion (XTri/Centromere linkage group) of chromosome 1D with anapparent positive effect brought by CS. For Blvol we revealed two QTLs inopposite phase: one in the Xtri/Centromere region with a positive effect ofCS allele, one in the Glu-D1 region with a positive effect of Cnnallele. This organization `in repulsion' in the parental lines could explain thesmall difference between them for Blvol and the significant transgressionobserved among the RSLs. No clear candidate gene explained the positiveeffect of the centromeric region of CS on %prot and Blvol. Contrary to thecurrent belief that wheat bread-making quality is determined primarily byvariation at the Glu-1 locus, present results showed that the trait isunder a complex control and the Glu-1 loci was only a component ofthe genetic control of the trait.     

Molecular mapping of major genes and quantitative trait loci determining flowering time in response to photoperiod in barley

Two major genes (eam8 and eam10) and two quantitative trait loci (QTL) determining flowering time in barley were associated with restriction fragment length polymorphism markers. The loci eam8 and eam10 were found to map in regions of chromosomes 1HL and 3HL, respectively, already estimated from previous classical linkage analyses. While investigating doubled haploid lines of a spring habit barley mapping population, two QTL for flowering time were detected on chromosomes 1HL and 7HS, respectively, when the material was grown under long photoperiod conditions. When growing the same lines under short photoperiod, no QTL were discernible. Allelic and homoeologous relationships with flowering time loci described earlier in barley and other Triticeae species are discussed.     

Characterization and mapping of gene Rph19 conferring resistance to Puccinia hordei in the cultivar 'Reka 1' and several Australian barleys

Previous studies established that the Australian barley cultivar ‘Prior’ possessed resistance to Puccinia hordei (RphP), displaying the same specificity as an uncharacterized resistance in the differential cultivar ‘Reka 1’ (also possessing Rph2). Multipathotype tests confirmed the presence RphP in nine additional barley cultivars and indicated that RphP differed in specificity to the genes Rph1 to Rph15 and Rph18, plus the gene RphX present in the barley cultivar ‘Shyri’. RphP was inherited as a single dominant gene. Mapping studies using a doubled haploid population derived from ‘Chebec’/‘Harrington’ located RphP to the long arm of chromosome 7H, and demonstrated linkage with an restriction fragment length polymorphism marker (pTAG732), a resistance gene analogue marker (RLch4(Nc)), and two microsatellite markers (HVM11 and HVM49) at genetic distances of about 4‐10 cM. RphP showed linkage of 28 ± 4.3 cM with Rph3. RphP was designated Rph19, with the allele designation Rph19.ah. Previous studies have established that virulence for Rph19 occurs in many barley growing regions of the world.     

QTL analysis and mapping of pre-harvest sprouting resistance in Sorghum

One of the most important agronomic problems in the production of sorghum [Sorghum bicolor (L.) Moench] in humid climates is pre-harvest sprouting (PHS). A molecular linkage map was developed using 112molecular markers in an F₂ mapping population derived from a cross between IS 9530 (high resistance to PHS) and Redland B2 (susceptible to PHS). Two year phenotypic data was obtained. By means of interval mapping analysis, two significant QTL were detected in two different linkage groups with LOD scores of 8.77and 4.39. Each of these two QTL individually explained approximately 53% of the phenotypic variance, but together, in a two-QTL model, they explained 83% of the phenotypic variance with a LOD score of 12.37.These results were corroborated by a one-way ANOVA in which the four flanking markers of the most likely QTL positions displayed highly significant values in theF-test, and significant variation in trait expression was associated with marker genotypic classes. The four markers with highest effect in the one-way ANOVA were also detected in the second year replication of the F₂ population, and significant genotype × environment interactions was observed. The putative relationship between PHS resistance in sorghum and the maize Vp1 gene is also discussed. This revised version was published online in July 2006 with corrections to the Cover Date.     

Mapping of QTL controlling NIR predicted hot water extract and grain nitrogen content in a spring barley cross using marker-regression

A restriction fragment length polymorphism (RFLP) map constructed from 99 doubled haploid lines of a cross between two spring barley varieties (‘;Blenheim’בKym’) was used to map QTL controlling hot water extract and grain nitrogen content (predicted by analysis with near-infrared reflectance spectroscopy). Eight QTL affecting predicted hot water extract were identified by a marker-regression approach. The largest effects were found on chromosomes 3HL, associated with the denso dwarfing gene which is present in‘Blenheim’and conferred poorer predicted hot water extract quality, and 4HL. Other QTL were detected on chromosomes IHS. IHL. 2HS, 2HL. 5HL and 6HS. Analysis of single markers by analysis of variance detected an additional effect on chromosome 1H. Eight QTL affecting predicted grain nitrogen content were identified by marker-regression, on chromosomes 1HS, 1HL. 2HL. 5HS, 6H, 7HS and 7HL. There was also evidence for an additional QTL on chromosome 5HL. The positions of the grain nitrogen content QTL on 5HS and 5HL are comparable to QTL on wheat chromosomes 5A and 5D that affect grain protein content. The denso gene had no detectable effect on grain nitrogen content.     

QTL mapping for heading date,leaf area and chlorophyll content under cold and drought stress in two related recombinant inbred line populations (Japonica rice) and meta‐analysis

Rice is highly susceptible to drought and cold. The goal of this study was to identify the QTLs affecting the rice heading date (HD), leaf area (LA) and chlorophyll content (CC) under cold and drought stress. A total of twenty‐nine and thirty‐eight additive QTLs were detected from two crosses of ‘Dongnong422’/‘Kongyu131’ and ‘Xiaobaijingzi’/‘Kongyu131’, respectively. qHD1‐7‐1, qHD1‐7‐2, qHD1‐2‐1, qLA1‐7‐1, qLA1‐6‐3 and qCC1‐7‐1 show adaptive effects under cold treatment, while qHD2‐2‐3, qHD2‐2‐2, qLA2‐7‐3 and qCC2‐5‐1 were important for explaining the genetic mechanism during drought tolerance. Additionally, nine and five additive × environment interaction QTLs were detected for two RILs, respectively. RIL26 and RIL73 were two lines that are associated with cold and drought for HD. 339 QTLs related to HD, CC and LA of rice from database and our research were projected onto the genetic map. Nine cloned genes and nineteen homologous candidate genes related to HD, CC, cold tolerance and drought tolerance were mapped by meta‐analysis. These results lay the foundation for the fine mapping of QTLs related to HD, LA and CC for marker‐assisted selection.     

Association of leaf rust and powdery mildew resistance in a recombinant derived from a Hordeum vulgare × Hordeum bulbosum hybrid

While studying powdery mildew resistance in a recombinant line (code 81882) derived from a Hordeum vulgare (cv. ‘Vada’) ×Hordeum bulbosum hybrid, a low infection type of resistance to leaf rust was observed. To determine the mode of inheritance of the leaf rust resistance and whether there was linkage between the two resistances, F₂ and F₃ progenies from crosses between 81882 and ‘Vada’ were inoculated with the leaf rust and powdery mildew pathogens. Southern blots were prepared using restricted DNA extracted from leaves of 82 F₂ plants and four chromosome 2HS sequences were hybridized with the blots to define the length of the introgression. The leaf rust resistance appears to be inherited as a single dominant gene on chromosome 2HS, which co-segregates with the powdery mildew resistance. There was an almost complete association between the resistances and the respective molecular markers, but it is likely that the strong linkage results from the frequent inheritance of the introgressed H. bulbosum DNA as an intact segment of chromatin with only low levels of recombination within the segment.     

Associations between 23 Quantitative Traits and 10 Genetic Markers in a Barley Cross

Associations of 23 quantitative traits and 10 genetic marker characters were examined in 63 chromosome-doubled lines (DH-lines) derived from the F₁- generation of a cross between an old and a modern spring barley variety. One fourth of the marker × trait combinations showed significant associations. More than two thirds of these associations were to earliness (heading date). Earliness was found to be controlled by two loci: the previously known eak locus and a new locus designated Ea. It is concluded that the associations of quantitative traits with the earliness loci were caused by pleiotropy. Associations were found between two absolutely linked C-bands on chromosome 3 and QTLs (quantitative trait loci) for lodging, straw diameter, and length of top internode of the straw. The three loci on chromosome 5, eak and the two linked powdery mildew loci, Mla9 and Mlk, were associated with a possible QTL for magnesium concentration in grain. Association to the C-band on chromosome 6 suggests QTLs for TGW (thousand grain weight), straw diameter and magnesium concentration in grain. Locus Estl on chromosome 3 was not associated with any of the quantitative traits.     

水稻白条纹叶突变体wsl1的遗传分析及基因精细定位

从粳稻日本晴和籼稻R1128杂交衍生的重组自交系群体中获得一个稳定遗传的白条纹叶突变体wsl1(white stripe leaf 1),世代为F10。与亲本R1128相比,突变体wsl1表现出白条纹叶,同时叶脉呈现白化,该性状在苗期就出现并持续整个生育期;突变体的株高、每穗总粒数、剑叶长、生育期显著增加,而结实率显著下降,其他农艺性状没有显著变化。分蘖期突变体wsl1的叶绿素a、叶绿素b和胡萝卜素含量较杂交亲本R1128显著下降;透射电镜观察表明,与野生型相比,突变体的叶绿体形状异常,不规则。遗传分析表明,该突变性状由1对隐性核基因控制。精细定位后发现,目标基因WSL1位于第1染色体短臂上标记M1-54与标记M1-70之间,两者相距89.7kb。生物信息学分析表明候选区间内共有8个开放阅读框,暂未发现已报道的叶色相关基因;其中LOC_Os01g02080编码肽基脯氨酰顺反异构酶,GO(Gene Ontology)分类显示其可能与类囊体形成有关,后续将通过比较测序、qRT-PCR等分子实验来确定候选基因。