Yield of doubled haploid lines of Nordic spring barley infected with net blotch, Pyrenophora teres

Five Nordic spring barley lines (‘Rolfi’, ‘Arve’, ‘Botnia’, ‘Pohto’ and WW7977) and doubled haploid (DH) populations from a half diallel of crosses between them, were sown in the field in Finland over 2 years and were artificially infected with Pyrenophora teres, the causal agent of net blotch. The purpose of the experiments was to determine the extent of yield loss under net blotch infection in a range of parent barleys and DH populations differing in symptom expression. Analysis of foliar damage symptoms, yield and aerial biomass data indicated that, in both years, there were statistically significant differences among parents and crosses, but the relationships between symptom expression and yield maintenance and between symptom expression and aerial biomass maintenance were stronger in 1997, when yields were higher and net blotch was less severe.     

QTL mapping of net blotch resistance genes in a doubled-haploid population of six-rowed barley

Net blotch, caused by Pyrenophora teres f. teres, is a damaging foliar disease of barley worldwide. It is important to identify resistance germplasm and study their genetics. 'Chevron', a six-rowed barley used as a parent for the production of a doubled haploid (DH) population for mapping of Fusarium head blight (FHB) resistance, was also found to be resistant to net blotch. To map the resistance genes, the population was evaluated for resistance at the seedling stage in a greenhouse. The resistance data showed a two-peak distribution. Through linkage mapping, one resistance gene, tentatively called Rpt, was located on chromosome 6HS flanked by Xksua3b-Xwg719d, which was also detected by QTL mapping. This QTL explained 64% of the phenotypic variance for the resistance in this DH population. In addition, a minor QTL was found on chromosome 2HS defined by Xcdo786-Xabc156a. 'Chevron' and 'Stander' contributed the resistant alleles of Rpt and the 2HS QTL, respectively. Both QTLs together explained nearly 70% of the phenotypic variance. The markers for these QTLs are useful for marker-assisted selection of net blotch resistance in barley breeding.     

Inheritance of resistance to Pyrenophora teres f. teres in spring barley

The inheritance of seedling resistance to a Swedish isolate of Pyrenophora teres f. teres was investigated in four resistance sources of spring barley. Accessions CI 2330, CI 5791, CI 5822 and CI 9779 were used as resistance sources, and the cultivar ‘Alexis’ was used as a susceptible parent in different crosses. From the disease reaction in the F₁, F₂ and F₃ generations it was concluded that the resistance was governed by the same two complementary genes in CI 5791, CI 822 and CI 9776. One of these genes was present in CI 2330. The first three cultivars were highly resistant to the isolate used in this investigation. These results, when combined with earlier studies, suggest that CI 5791, CI 5822 and CI 9776 may be of great value as sources of resistance to barley net blotch. Spearman's rank correlation between the disease reaction of F₂ plants and their F₃ progeny was highly significant (r = 0.75; P ≥ 0.001) It is suggested that selection in the F₂ generation is effective. In a backcross breeding scheme, single plant reactions in F₁ or F₂ need to be confirmed in later generations.     

Localization of the Laevigatum Resistance Gene MlLa against Powdery Mildew in the Barley Genome by the Use of RFLP Markers

RFLP markers which were previously assigned to chromosome 2 (2H) were found to detect polymorphism between the cv. ‘Pallas’ and a near isogenic line carrying the Laevigatum resistance gene MlLa. Linkage analysis carried out with two sets of DH lines derived from the crosses ‘RisøS’בSultan’ and ‘Alf’בVogelsanger Gold 2’ confirmed three DNA probes closely linked with the MlLa locus.     

Diallel analysis of net blotch resistance in doubled haploid lines of Nordic spring barleys

A half-diallel was made between five six-rowed Nordic spring barleys to study the genetics of resistance to net blotch. Twenty-five doubled-haploid (DH) lines from each cross and the parents were sown in hill plots in Finland in 1997 and 1998. The plots were artificially inoculated with Pyrenophora teres Drechs. f. teres Smedeg. and assessed for resistance to net blotch. There were statistically significant differences in resistance of the five parents to net blotch. General combining ability (GCA) of the parents and specific combining ability (SCA) effects in the progeny were statistically significant in both years, but GCA effects predominated. Evidence for additive epistasis was minimal. Progeny of a particular cross were less resistant to net blotch than the better parent. The most resistant progeny were derived from the cross between the two most resistant parents, Pohto and WW7977, and resistance was governed by at least eleven effective factors. Narrow sense heritability estimates for resistance to net blotch were high during both years (0.84–0.99). It appears that net blotch resistance of progeny from crosses can be largely predicted from reactions of the parents. Quantitative resistance to net blotch can be further advanced by identification and incorporation of superior parents, from a screening such as reported here, into a recurrent selection breeding programme. This revised version was published online in August 2006 with corrections to the Cover Date.     

Generation Mean Analysis of Inheritance of Resistance to Pyrenophora teres in Barley

F1, F2, Fl × parentl (BC1), and Fl × parent2 (BC2) generations resulting from four crosses among seven cultivars of barley used in national and international breeding programmes were tested at the seedling stage for their resistance to a mixture of five isolates of Pyrenophora teres. Four methods were used to assess disease resistance: infection type (IT), average lesion size (ALS), number of lesions per unit leaf area (NL) and percent leaf area infected (PLAI). Gene actions were estimated by generation mean analysis on each of the four crosses and on each of the evaluation methods. Significant additive and additive × additive epistatic effects were found. Infection type and percent leaf area infected were found to be highly correlated in all four crosses. These results suggest that barley breeders could improve the level of resistance to P. teres by making appropriate crosses between highly susceptible barley cultivars.     

Mapping quantitative trait loci controlling pre-harvest sprouting resistance in a red × white seeded spring wheat cross

Hard white wheat (Triticum aestivum L.) is a value-added product because of its processing advantages over red wheat; however, white wheat tends to be more susceptible to pre-harvest sprouting (PHS). To identify quantitative trait loci (QTLs) associated with PHS tolerance, we developed a doubled haploid (DH) mapping population from the cross AC Domain (red seeded) × White-RL4137 (white seeded). A genetic map was constructed using microsatellite markers located on chromosome groups 3, 4, 5 and 6. A population of 174 DH lines was characterized for important aspects of PHS including sprouting index, germination index, Hagberg falling number and seed coat colour. A total of 11 QTLs were identified on group 3 chromosomes and on chromosome 5D. Seven QTLs associated with the PHS traits were found to be co-incident with seed coat colour on chromosomes 3A, 3B and 3D. The 5D PHS QTL was notable because it is independent of seed coat colour.     

Molecular mapping of QTLs for non-parasitic leaf spot resistance and comparison of half-sib DH populations in spring barley

Quantitative trait loci (QTLs) for resistance against non-parasitic leaf spots (NPLS) were first characterized in a spring barley double haploid population derived from the cross IPZ 24727/Barke (Behn et al., 2004). The aim of the present study was to identify QTLs for NPLS resistance in the half-sibling DH population IPZ 24727/Krona and to compare them with the QTLs of the population IPZ 24727/Barke. An anther culture-derived doubled haploid population of 536 DH lines was developed from the cross IPZ 24727 (resistant)/Krona (susceptible). Field trials were performed over two years in two replications, scoring NPLS and agronomic traits that might interact with NPLS. A molecular linkage map of 1035 cM was constructed based on AFLPs, SSRs and the mlo marker. QTL analyses for NPLS identified three QTLs that accounted for 30% of the phenotypic variation. For comparison of the QTLs from each DH population, a consensus map was generated comprising 277 markers with a length of 1199 cM. In both populations, the QTLs for NPLS mapped to chromosomes 1H, 4H and 7H. A common QTL with a great effect in both populations and over all environments was localized at the mlo locus on chromosome 4H, indicating that the mlo powdery mildew resistance locus has a considerable effect on NPLS susceptibility. The steps necessary to validate the QTLs and to improve the NPLS resistance by breeding were discussed.     

Mapping quantitative trait loci (QTLs) underlying seed vitamin E content in soybean with main,epistatic and QTL × environment effects

Soybean (Glycine max (L.) Merr.) seed contains small amounts of tocopherol, a non‐enzymatic antioxidant known as lipid‐soluble vitamin E (VE). Dietary VE contributes to a decreased risk of chronic diseases in humans and has several beneficial effects on resistance to stress in plants, and increasing VE content is an important breeding goal for increasing the nutritional value of soybean. In this study, quantitative trait loci (QTLs) underlying VE content with main, epistatic and QTL × environment effects were identified in a population of F_5 : 6 recombinant inbred lines from a cross between ‘Hefeng 25’ (a low‐VE cultivar) and ‘OAC Bayfield’ (a high‐VE cultivar). A total of 18 QTLs were detected that showed additive main effects (a) and/or additive × environment interaction effects (ae) in different environments. Moreover, 19 epistatic pairs of QTLs were found to be associated with α‐tocopherol (α‐Toc), γ‐tocopherol (γ‐Toc), δ‐tocopherol (δ‐Toc) and total VE (TE) contents. The QTLs identified in multienvironments could provide more information about QTL by environment interactions and could be useful for the marker‐assistant selection of soybean cultivars with high seed VE contents.     

Comparison and analysis of main effects,epistatic effects,and QTL × environment interactions of QTLs for agronomic traits using DH and RILs populations in rice

Two genetic linkage maps based on doubled haploid (DH) and recombinant inbred lines (RILs) populations, derived from the same indica-japonica cross ‘Samgang × Nagdong’, were constructed to analyze the quantitative trait loci (QTLs) affecting agronomic traits in rice. The segregations of agronomic traits in RILs population showed larger variations than those in DH population. A total of 10 and 12 QTLs were identified on six chromosomes using DH population and seven chromosomes using RILs population, respectively. Three stable QTLs including pl9.1, ph1.1, and gwp11.1 were detected through different years. The percentages of phenotypic variation explained by individual QTLs ranged from 8 to 18% in the DH population and 9 to 33% in the RILs population. Twenty-three epistatic QTLs were identified in the DH population, while 21 epistatic QTLs were detected in the RILs population. Epistatic interactions played an important role in controlling the agronomic traits genetically. Four significant main-effect QTLs were involved in the digenic interactions. Significant interactions between QTLs and environments (QE) were identified in two populations. The QTLs affecting grain weight per panicle (GWP) were more sensitive to the environmental changes. The comparison and QTLs analysis between two populations across different years should help rice breeders to comprehend the genetic mechanisms of quantitative traits and improve breeding programs in marker-assisted selection (MAS).     

A comparison of grain protein content QTLs and flour protein content QTLs across environments in cultivated wheat

The protein content of cultivated wheat (Triticum aestivum L.) is an important determinant factor of the nutritional value of the grain and the technological properties and rheological properties of flour. In order to examine the genetic basis of protein content, we searched for grain protein content quantitative trait loci (QTLs) and flour protein content QTLs in a newly developed doubled haploid (DH) line and identified the genetic correlation between grain protein content and flour protein content in the same DH population. Both the DH population and its parental lines were evaluated for grain protein content and flour protein content in three field trials. Four additive effect QTLs, two pairs of epistatic QTLs, and two QTLs × environment (QE) interaction for grain protein content were identified. The model explained 51.52% of the phenotypic variation (PVE), with epistatic effects being better explained by the higher PVE than additive effects. Four additive effect QTLs, five pairs of epistatic QTLs, and one QE were detected for flour protein content. The model explained 45.8% of the PVE. Of the 15 QTLs identified, three additive QTLs and one pair of epistatic QTLs were determined for both grain protein content and flour protein content; of these, the QTLs for protein content were considered to be more 'stable' than those detected for only grain protein content or for only flour protein content. The data reported here may be useful for manipulating the QTLs for protein content by marker-assisted selection in future wheat breeding programs.     

Fine mapping of a QTL for the number of spikelets per panicle by using near‐isogenic lines derived from an interspecific cross between Oryza sativa and Oryza minuta

We constructed a high‐resolution physical map for the qSPP7 QTL for spikelets per panicle (SPP) on rice chromosome 7 across a 28.6‐kb region containing four predicted genes. Using a series of BC₇F₄ near‐isogenic lines (NILs) derived from a cross between the Korean japonica cultivar ‘Hwaseongbyeo’ and Oryza minuta (IRGC Acc. No. 101144), three QTLs for the number of SPP, grains per panicle and primary branches were identified in the cluster (P ≤ 0.01). All three QTLs were additive, and alleles from the O. minuta parent were beneficial in the ‘Hwaseongbyeo’ background. qSPP7 was mapped to a 28.6‐kb region between the two simple sequence repeat (SSR) markers RM4952 and RM21605. The additive effect of the O. minuta allele at qSPP7 was 23 SPP, and 43.6% of the phenotypic variance was explained by the segregation of the SSR marker RM4952. Colocalization of the three QTLs suggested that this locus was associated with panicle structure and had pleiotropic effects. The NIL populations and molecular markers are useful for cloning qspp7.     

Development of molecular markers for crown rot resistance in wheat: mapping of QTLs for seedling resistance in a '2-49' × 'Janz' population

Crown rot, caused by Fusarium pseudograminearum, is an important disease of wheat in Australia and elsewhere. In order to identify molecular markers associated with partial seedling resistance to this disease, bulked segregant analysis and quantitative trait loci (QTL) mapping approaches were undertaken using a population of 145 doubled haploid lines constructed from ‘2‐49’ (partially resistant) × ‘Janz’ (susceptible) parents. Phenotypic data indicated that the trait is quantitatively inherited. The largest QTLs were located on chromosomes 1D and 1A, and explained 21% and 9% of the phenotypic variance, respectively. Using the best markers associated with five QTLs identified by composite interval mapping, the combined effect of the QTLs explained 40.6% of the phenotypic variance. All resistance alleles were inherited from ‘2‐49’ with the exception of a QTL on 2B, which was inherited from ‘Janz’. A minor QTL on 4B was loosely linked (19.8 cM) to the Rht1 locus in repulsion. None of the QTLs identified in this study were located in the same region as resistance QTLs identified in other populations segregating for Fusarium head blight, caused by Fusarium graminearum.     

Identification of QTLs for powdery mildew and scald resistance in barley

A population of 103 recombinant inbred lines (RILs, F₉-derived lines) developed from the two-row spring barley cross L94 × ‘Vada’ was evaluated under field conditions for resistance against powdery mildew (Blumeria graminis f.sp. hordei) and scald (Rhynchosporium secalis). Apart from the major resistance gene mlo on chromosome 4 (4H), three QTLs (Rbgq1, Rbgq2 and Rbgq3) for resistance against powdery mildew were detected on chromosomes 2 (2H), 3 (3H), and 7 (5H), respectively. Rbgq1 and Rbgq2 have not been reported before, and did not map to a chromosome region where a major gene for powdery mildew had been reported. Four QTLs (Rrsq1, Rrsq2, Rrsq3 and Rrsq4) for resistance against scald were detected on chromosomes 3 (3H), 4 (4H) and 6 (6H). All four mapped to places where QTLs for scald resistance had been reported before in different populations.     

QTL analysis of textural property traits for Chinese northern-style steamed bread

Quantitative trait loci (QTLs) influencing textural properties (hardness, adhesiveness, springiness, cohesiveness, gumminess, chewiness, and resilience)of wheat for Chinese northern-style steamed bread were studied using a doubled haploid (DH) population containing 168 lines derived from a cross between elite Chinese wheat cultivars Huapei 3 and Yumai 57 (Triticum aestivum L.). The DH population and parents were grown in 2007 and 2008 in Tai’an and 2008 in Suzhou. QTL analyses were performed using the software QTL Network version 2.0 and IciMapping v2.2 based on the mixed linear model. Thirty nine putative QTLs were detected on 14 chromosomes: viz. 1A, 2A, 3A, 4A, 6A, 1B, 2B, 3B, 5B, 6B, 7B, 5D, 6D, and 7D, and single QTLs explained 3.91–35.17% of the phenotypic variation. Eight pairs of QTLs with epistatic effects and/or epistasis × environment (AAE) effects were detected for adhesiveness, resilience, hardness, and cohesiveness on chromosomes 2A, 1B and 3D. Several co-located QTLs with additive effects were detected on chromosomes 2B, 5D, 6A, 3A, 3B and 6D. Two clusters of three QTLs for steamed bread textural properties (chewiness, gumminess, and hardness) and for adhesiveness, cohesiveness and resilience were detected on chromosome 2B. Two co-located QTLs with epistatic effects were detected on chromosomes 1B and 3A. Both additive effects and epistatic effects were important for Chinese steamed bread textural properties, which were also subject to environmental modifications. The information obtained in this study will be useful for manipulating QTLs determining Chinese steamed bread textural properties by molecular marker-assisted selection.     

Identification and validation of an over‐dominant QTL controlling soybean seed weight using populations derived from Glycine max × Glycine soja

Heterosis, or hybrid vigour, has been used to improve seed yield in several important crops for decades and it has potential applications in soybean. The discovery of over‐dominant quantitative trait loci (QTL) underlying yield‐related traits, such as seed weight, will facilitate hybrid soybean breeding via marker‐assisted selection. In this study, F₂ and F_2 : 3 populations derived from the crosses of ‘Jidou 12’ (Glycine max) × ‘ZYD2738’ (Glycine soja) and ‘Jidou 9’ (G. max) × ‘ZYD2738’ were used to identify over‐dominant QTL associated with seed weight. A total of seven QTL were identified. Among them, qSWT_13_1, mapped on chromosome 13 and linked with Satt114, showed an over‐dominant effect in two populations for two successive generations. This over‐dominant effect was further examined by six subpopulations derived from ‘Jidou12’ × ‘ZYD2738’. The seed weight for heterozygous individuals was 1.1‐ to 1.6‐fold higher than that of homozygous individuals among the six validation populations examined in different locations and years. Therefore, qSWT_13_1 may be a useful locus to improve the yield of hybrid soybean and to understand the molecular mechanism of heterosis in soybean.     

Genetic analysis and quantitative trait locus mapping of PEG‐induced osmotic stress tolerance in cotton

Water stress is one of the major abiotic stresses that adversely affect cotton production. Seedlings of 142 backcross inbred lines (BILs) derived from Pima cotton ‘Pima S‐7’ (Gossypium barbadense L.) × Upland cotton ‘Sure‐Grow 747’(G. hirsutum L.) were evaluated in two tests for plant height, fresh shoot weight and root weight under two treatments (5% PEG and water‐control conditions) using a hydroponic system in the greenhouse. The experiment in each test was a randomized complete block design with three replicates. The analysis of variance for the two tests detected significant genotypic variation in PEG‐induced stress tolerance within the BIL population and between the parents. Heritabilities were moderate to high and were higher under the control conditions than under the PEG treatment, and the three traits were also significantly and positively correlated. Based on a linkage map with 292 loci, six QTLs were detected including two for plant height, and two each for fresh shoot weight and root weight. This study represents the first report in using a permanent mapping population in genetic and linkage analysis of water stress tolerance in cotton.     

QTL alleles from a winter feed type can improve malting quality in barley

Mapping quantitative trait loci (QTLs) responsible for malting quality traits in barley populations has been the main genetic approach to malting quality breeding. A ‘winter × spring’ doubled haploid barley population ‘Nure’ × ‘Tremois’, where such traits were segregating, has been recently developed. Our objective was to map QTLs for malting quality from 2 years of trials in two contrasting locations. QTLs were found on six chromosomes, with a main cluster on chromosome 1H. For wort viscosity and malt extract, favourable alleles at two loci on chromosome 5H were carried by the winter feeding parent ‘Nure’. Doubled‐haploids with higher quality than the spring malting cultivar ‘Tremois’ showed either a facultative or a winter growth habit and a level of frost tolerance comparable with that of the winter tolerant parent ‘Nure’. Markers and QTLs of quality traits were further validated on a separate set of DH lines, coming from the same cross, by means of marker‐assisted selection. This showed that, at least in the present cross combination, positive contributions to malting quality can be found in winter feed barley.     

The validation of two major QTLs related to the timing of spring bud flush in <Emphasis Type="Italic">Camellia sinensis</Emphasis>

The timing of spring bud flush (TBF) in tea plants (Camellia sinensis) is an adaptive critical and economically important trait; thus, it has been a focus of many tea-breeding programs. Previously, we reported the mapping of two major and partial linked TBF QTLs onto the LG01 of C. sinensis using a full-sib population of ‘Longjing 43’ × ‘Baihaozao’. In this study, we further tested the QTL stability and expression variation in different years, experimental sites, and crossing parents. We genotyped 157 additional F₁ individuals from the ‘Longjing 43’ × ‘Baihaozao’ cross and 173 F₁ individuals from ‘Wuniuzao’ × ‘Longjing 43’ cross with 16 and 17 SSR markers on LG01, respectively. We also recorded the TBF trait of the two populations at Hangzhou and/or Shengzhou sites in the spring of 2014, 2015 and/or 2017. The TBF QTLs were significant (P < 0.001 at the chromosome-wide level) in all tested years, sites, and populations, but the explained phenotypic variation ranged considerable (26.2–40.5%, two QTLs were considered together in the Interval Mapping). Interestingly, the QTLs only segregated in ‘Longjing 43’ among the three parents involved. After grouping the individuals by the genotypes of the two markers closest to the QTLs, a maximum difference of 9.22 days for the average TBF was observed between the earliest and latest groups.     

Construction of high-density linkage map and identification of QTLs associated with resistance to black rot in radish (Raphanus sativus) by RAD sequencing

High-density marker-based QTL mapping can serve as an effective strategy to identify novel genomic information to facilitate crop improvement. In this study, we genotyped an F₂ population (KB12-1 × PP12-1) using a RAD-seq approach and constructed a high-density linkage map for radish. After a series of filtering procedures were performed, 17,124 SNPs and 3,336 indels with aa × bb genotyping were retained to obtain bin markers. Then, a linkage map comprising a total of 1,221 bin markers in nine linkage groups spanning 1,467.3 cM with an average marker interval of 1.2 cM was constructed. We evaluated the resistance of the F₂ mapping population to black rot using F₃ progeny, and two major QTLs related to black rot resistance were identified based on this map. Among these QTLs, qBRR2 on Chr.2 explained 26.97% of the phenotypic variation with a LOD score of 11.93, and qBRR7 on Chr.7 accounted for 27.06% of the phenotypic variation with a LOD score of 11.83. The additive effect of qBRR2 was positive (14.97); however, qBRR7 had the opposite effect (−11.99). The high-density linkage map and the major QTLs qBRR2 and qBRR7 provide new important information for disease resistance gene discovery and utilization in genetic improvement.