Mapping QTLs with epistatic effects and QTL × treatment interactions for salt tolerance at seedling stage of wheat

Quantitative trait loci (QTLs) with additive (a), additive × additive (aa) epistatic effects, and their treatmental interactions (at and aat) were studied under salt stress and normal conditions at seedling stage of wheat (Triticum aestivum L.). A set of 182 recombinant inbred lines (RILs) derived from cross Xiaoyan 54 × Jing 411 were used. A total of 29 additive QTLs and 17 epistasis were detected for 12 traits examined, among which eight and seven, respectively, were identified to have QTL × treatment effects. Physiological traits rather than biomass traits were more likely to be involved in QTL × treatment interactions. Ten intervals on chromosomes 1A, 1D, 2A (two), 2D, 3B, 4B, 5A, 5B and 7D showed overlapping QTLs for different traits; some of them represent a single locus affecting different traits and/or the same trait under both treatments. Eleven pairs of QTLs were detected on seemingly homoeologous positions of six chromosome groups of wheat, showing synteny among the A, B and D genomes. Ten pairs were detected in which each pair was contributed by the same parent, indicating a strong genetic plasticity of the QTLs. The results are helpful for understanding the genetic basis of salt tolerance in wheat and provide useful information for genetic improvement of salt tolerance in wheat by marker-assisted selection.     

Mapping QTLs associated with Fusarium-damaged kernels in the Nanda 2419 × Wangshuibai population

Fusarium head blight (FHB), or scab, is a devastating wheat disease worldwide, reducing both grain yield and quality. The percentage of Fusarium-damaged kernels (FDK) directly reflects the damage level caused by scab on wheat grains and its variation represents the so-called type IV scab resistance in germplasm. To identify genes governing type IV resistance and investigate its relationship with other scab resistance types, we mapped QTLs associated with percent FDK using data from three different field evaluations of the recombination inbred line (RIL) population derived from the susceptible cultivar Nanda 2419 × the scab-resistant cultivar Wangshuibai. Five QTLs related to percent FDK were identified in at least two different trials, for which Wangshuibai contributed four of the resistance alleles. Most of the FDK-related QTLs, including the three with larger effects, QFdk.nau-2B, QFdk.nau-3B and QFdk.nau-4B, mapped to intervals associated with either type IV resistance or type II resistance. Moreover, most of the major type I and type II resistance QTLs detected previously were associated with type IV resistance, suggesting that resistance to initial infection and disease spread play major roles in conditioning less FDK. Therefore, breeders have options to choose inoculation methods based on their expertise and resources without risking significant loss of information when using percent FDK as the disease index. The most useful scab resistance QTLs for breeding would be those with stable influences on FDK and/or deoxynivalenol (DON) accumulation besides the initial infection and disease spread. Chunjun Li and Huilan Zhu contributed equally to this work.     

QTL analysis for eating quality-related traits in an F2:3 population derived from waxy corn × sweet corn cross

In order to identify quantitative trait loci (QTL) for the eating quality of waxy corn and sweet corn (Zea mays L.), QTL analysis was conducted on an F₂ population derived from a cross between a waxy corn inbred line and a sweet corn inbred line. Ten QTLs for pericarp thickness (PER), amylose content (AMY), dextrose content (DEX) and sucrose content (SUC) were found in the 158 F₂ families. Among them, four QTLs, qAMY4 (10.43%), qAMY9 (19.33%), qDEX4 (21.31%) and qSUC4 (30.71%), may be considered as major QTLs. Three of these, qAMY4, qDEX4 and qSUC4, were found to be located within a region flanked by two adjacent SSR markers on chromosome 4 (umc1088 and bnlg1265), making this SSR marker pair a useful selection tool for screening the eating quality traits of AMY, DEX and SUC. The QTL for amylose content was found to be located between markers phi027 and umc1634, raising the possibility of its identity being the Wx1 gene, which encodes a granule-bound amylose synthase. The new QTLs identified by the present study could serve as useful molecular markers for selecting important eating quality traits in subsequent waxy corn breeding studies.     

Genetic analysis of drought tolerance in adapted × exotic crosses of maize inbred lines under managed stress conditions

Introduced maize (Zea mays L.) germplasm can serve as sources of favorable alleles to enhance performance in new maize varieties and hybrids under drought stress conditions. In the present study, the combining abilities of 12 exotic maize inbred lines from CIMMYT and 12 adapted maize inbred lines from IITA were studied for grain yield and other traits under controlled drought stress. The inbred lines from each institution were separated into groups using SSR-based genetic diversity and were intercrossed using a factorial mating scheme to generate 96 hybrids. These hybrids were evaluated under both controlled drought stress and well-watered conditions at Ikenne in Nigeria in 2010 and 2011. Average mean yields of hybrids under drought stress represented 23 % of the average yield of hybrids under full irrigation. General combining ability (GCA) effects accounted for 49–85 % of the observed variation for several traits recorded under both well-watered and drought stress conditions. Specific combining ability effects for grain yield, though positive in most hybrids, were not significant under drought stress conditions. All the twelve exotic and nine adapted lines had positive GCA effects (female, male, or both) for grain yield under either drought stress or full irrigation, or both environments. EXL03 and EXL15 that had positive and significant female and male GCA effects for grain yield under both environments can be used to improve their adapted counterparts for grain yield and drought tolerance. Normalized difference vegetation index had weak but significant correlation with grain yield.     

Plant age and in vitro or in vivo propagation considerably affect cold tolerance of Miscanthus × giganteus

The aims of the study were to determine why young Miscanthus × giganteus plants are more frost sensitive during the first winter than older plants, to compare cold tolerance of plants propagated in in vivo and in vitro conditions, and to select plants with higher cold tolerance. The study was performed in three experiments in which plants were prehardened at 12 °C for 2 weeks, hardened at 5 °C for 3 weeks and next chilled at 0 °C or ?3 °C for 3 or 14 days. Afterwards shoot regrowth from rhizomes was evaluated. In Experiment 1 frost tolerance of young plants obtained from a horticultural farm and plants that had already survived the first winter in the field was compared on the basis of LT₅₀ coefficient. In Experiment 2 frost tolerance of plants obtained in vivo and in vitro was compared. Experiment 3 was performed on four groups of plants: in vivo and in vitro obtained plants which were twice selected in cold, as well as in vivo and in vitro obtained plants which were cold treated once. Plants of all these groups were analysed with respect to their frost tolerance. They were prehardened, hardened and subjected to a temperature of 0 °C or ?3 °C for 14 days. The changes in processes accompanying cold acclimation occurring in the rhizomes or leaves of these plants were investigated. The content of abscisic acid, low-molecular antioxidants and phenolics, as well as catalase and non-specific peroxidase activities were analysed.Young commercially obtained plants were more frost sensitive than plants which had survived the first winter in the field. This effect could be caused by a small amount of storage compounds accumulated in finely divided rhizomes produced in a horticultural farm. Prehardening temperature of 12 °C caused more considerable changes in cold acclimation processes in Miscanthus rhizomes than hardening temperature of 5 °C. Plants propagated by in vitro culture were more cold tolerant but only in the first vegetative season compared to plants obtained in vivo. Plants chilled twice demonstrated a higher low-molecular antioxidant level, as well as a greater capability of phenolic accumulation compared to plants which were once cold stressed. Regardless of the recurrence of cold acclimation, ABA level was significantly increased in leaves by prehardening and in rhizomes by hardening. Each repetition of cold acclimation increased cold tolerance and shoot regeneration ability of M. × giganteus rhizomes.     

Inheritance of field resistance to Septoria tritici blotch in the wheat doubled-haploid population Solitär × Mazurka

Breeding for field resistance to Septoria tritici blotch (STB), caused by Mycosphaerella graminicola (anamorph: Septoria tritici), is the most suitable strategy for controlling this important disease of wheat. Although many Stb genes for resistance to single pathogen isolates have been identified in wheat, knowledge of their efficiency against natural fungal populations is lacking. In a quantitative-trait-locus (QTL) mapping approach in six environments and four locations, field resistance to STB was studied in a doubled-haploid population derived from a cross between the field-resistant cultivar Solitär and the susceptible cultivar Mazurka. After plant height as a disease escape trait was accounted for, five QTL with effects on STB response on chromosomes 5A, 6D and 7D explained 20 % of the genotypic variance; QTL × environment interactions were minor. Field resistance was conferred exclusively by alleles from Solitär, which was previously shown to carry the isolate-specific genes Stb6 and Stb11 as well as minor QTL detected with seven fungal isolates. Surprisingly, neither the Stb6 nor Stb11 isolate-specific genes nor minor QTL previously detected in Solitär were found to be involved in its field resistance. The study suggests that resistance breeding for STB should not rest solely on the deployment of Stb genes. Field tests are indispensable to show their efficacy and durability and to identify genes conferring partial field resistance to STB.     

Identification of QTLs Affecting Yield and Fiber Properties in Chromosome 16 in Cotton Using Substitution Line

Gossypium hirsutum L., one of the twocultivated tetraploid species in cotton,ischaracterized by its high yield and wideadaptation,while G.barbadense L.,anothercultivated one,by its super fiber properties.Substitution line in which one pair of intact     

Morphological and physiological behaviour of sweet cherry ‘somaclone’ HS plants in field

We reported earlier that somaclonal variant HS (HS), regenerated from Prunus avium `Hedelfinger’ (H) leaf explants, showed reduced apical dominance both in vitro and in vivo. In this report we found that the somaclone HS, showed reduced vegetative vigour as determined by trunk circumference and tree height nevertheless natural architecture of the tree was preserved. HS canopy was less crowded as to compare to H and leaves were shorter with a shorter petiole, they were better spaced out as indicated by internodes length. HS had a significantly thinner cuticle and wax layer compared to H leaves surface. Histological analysis of leaves also showed that HS had thicker mesophyll and palisade the latter composed of more than one layer which, together with increased stomatal density, are distinguishing signs of extensive exposure of leaves to sun. Chlorophyll a and chlorophyll b content did not differ between H and HS, β-carotene content was slightly lower in HS leaves. However no significant differences were found between the two genotypes in terms of net photosynthesis, intercellular CO₂ concentration, leaf transpiration and water use efficiency. HS flowered 1-year later than H and number of flowers was reduced. Fruit size, shape, skin colour change during the ripening process and the main parameters of fruit quality as assessed in the wild type and the somaclone were basically the same.     

Epistasis in an Andean × Mesoamerican cross of common bean

The objective of this investigation was to check if epistasis is present in Andean × Mesoamerican beans crosses using triple test cross (TTC) method. The parents of the segregating population were Carioca–MG (Mesoamerican) and BRS Radiante (Andean). In July 2005, F₂ progenies (backcrossed with the parents and F₁ generation) were evaluated at two locations for three characters: number of pods plant⁻¹, number of grains plant⁻¹ and grain weight plant⁻¹. The presence of epistasis was detected for all yield components. In the partitioning of epistasis in additive x additive (i) and dominant x dominant (j) and dominant × additive (l) it was observed that, for the traits number of pods/plant and number of grains/plant, only epistasis of the type (j) + (l) were significant. For the trait grain mass/plant, all types of epistasis were significant.     

QTLs for barley yield adaptation to Mediterranean environments in the ‘Nure’ × ‘Tremois’ biparental population

Multi-environment trials represent a highly valuable tool for the identification of the genetic bases of crop yield potential and stress adaptation. A Diversity Array Technology^®-based barley map has been developed in the ‘Nure’ × ‘Tremois’ biparental Doubled Haploid population, harbouring the genomic position of a gene set with a putative role in the regulation of flowering time and abiotic stress response in barley. The population has been evaluated in eighteen location-by-year combinations across the Mediterranean basin. QTL mapping identified several genomic regions responsible for barley adaptation to Mediterranean conditions in terms of phenology, grain yield and yield component traits. The most frequently detected yield QTL had the early flowering HvCEN_EPS2 locus (chromosome 2H) as peak marker, showing a positive effect from the early winter parent ‘Nure’ in eight field trials, and explaining up to 45.8 % of the observed variance for grain yield. The HvBM5A_VRN-H1 locus on chromosome 5H and the genomic region possibly corresponding to PPD-H2 on chromosome 1H were significantly associated to grain yield in five and three locations, respectively. Environment-specific QTLs for grain yield, and clusters of yield component QTLs not related to phenology and or developmental genes (e.g. on chromosome 4H, BIN_09) were observed as well. The results of this work provide a valuable source of knowledge and tools for both explaining the genetic bases of barley yield adaptation across the Mediterranean basin, and using QTL-associated markers for MAS pre-breeding and breeding programmes.     

Identification of QTLs for stay green trait in wheat (<Emphasis Type="Italic">Triticum aestivum</Emphasis> L.) in the ‘Chirya 3’ × ‘Sonalika’ population

Stay green or delayed senescence is considered to play a crucial role in grain development in wheat when assimilates are limited. We identified three QTLs for stay green on the chromosomes 1AS, 3BS and 7DS using a recombinant inbred (RI) population developed by making crosses between the stay green parent ‘Chirya 3’ and non-stay green ‘Sonalika’. The RI lines were evaluated in natural field conditions for 2 years in replicated trial. The QTL on chromosome 1A was identified in both the years, while the QTLs on 3BS and 7DS were identified only in 1st and 2nd year, respectively. The QTLs explained up to 38.7% of phenotypic variation in a final simultaneous fit. The alleles for higher stay green values derived from the stay green parent ‘Chirya 3’. The QTLs were named as QSg.bhu-1A, QSg.bhu-3B and QSg.bhu-7D. The QTL QSg.bhu-3B and QSg.bhu-7D were placed in the 3BS9-0.57-0.78 and 7DS5-0.36-0.61 deletion bins, respectively.     

Performance of upland coloured cotton germplasm lines in line × tester crosses

Anthracnose is a serious disease affecting dry bean production especially in the cool highland areas worldwide. The objective of this research was to study the inheritance of anthracnose resistance in market-class dry beans. A complete diallel set of crosses was generated from nine diverse parents comprising six resistant and three susceptible to anthracnose. The F₁ and F₂ crosses and parents were artificially inoculated with Colletotriclum lindenumthianum Race-767 in a growth room. There was significant variation for anthracnose resistance among genotypes. General combining ability (GCA) and specific combining ability effects were significant for resistance, indicating importance of both additive and non-additive effects, respectively. Preponderance of GCA effects (66%) suggested that additive effects were more important than non-additive effects (24%), which were also reflected by high heritability estimates (70%), and suggested that simple selection or backcrossing would be useful for improving the resistance in market class varieties. The study was not conclusive on whether epistatic gene action played a major role, but if available it might have biased the dominance gene effects. Reciprocal effects (10%) were not significant (P > 0.05), suggesting that cytoplasmic genes did not play a major role in modifying anthracnose resistance. Parental lines G2333, AB136, NAT002, and NAT003 showed highly negative GCA effects qualifying them as suitable parents for transferring resistance genes to their progenies. A few major genes, 1–3, displaying partial dominance conditioned anthracnose resistance, suggesting a possibility of using marker-assisted selection to improve anthracnose resistance in market-class dry beans.     

Parental effects on the performance of cultivated × wild species hybrids in potato

Valuable genetic diversity in diploid wild Solanum species can be accessed through crosses to haploids (2n = 2×) of the tetraploid cultivated potato, Solanum tuberosum. Haploid-wild species hybrids segregate for the ability to tuberize in the field. In addition, they vary in male fertility, vine size, stolon length, and tuber size. In this study, three haploids were crossed with nine diploid wild Solanum species and 27 hybrid families were evaluated in the field for two years. The proportion of male fertile hybrid clones varied depending on the wild species parent. A large effect of the female parent was detected for vine size, stolon length, tuber size, percent tuberization, and percent plants selected for agronomic quality. An exceptional haploid (US-W4) was identified for the production of agronomically desirable haploid-wild species hybrids. In hybrids derived from US-W4, differences among wild species parents were observed for agronomic quality. Superior hybrids were produced by S. berthaultii and S. microdontum. Reciprocal crosses were evaluated for a subset of families. When the wild species was used as the female parent, male fertility was restored, but tuberization and tuber size were reduced. Careful selection of both haploid and wild species parents can result in a large proportion of fertile, agronomically desirable hybrid offspring.     

Inheritance of anthocyanin content in the ripe berries of a tetraploid × diploid grape cross population

Variation patterns and inheritance of anthocyanin content in the ripe berries of a tetraploid × diploid table grape cross population were investigated in two successive years. The population segregated for three different ploid levels: dipolids, triploids, and tetraploids. A total of 28 different anthocyanins were detected and quantified in the progeny population. Transgressive segregation for the total anthocyanin content was observed in all the three ploid progeny populations. The total anthocyanin content increased as the ploid level increased. The broad sense heritabilities (H²) of the total anthocyanin content were all relatively high, ranging from 0.53 to 0.98, 0.57 to 0.97 and 0.43 to 0.94 in the diploid, triploid and tetraploid population, respectively. Our results suggested that the total anthocyanin content followed an additive inheritance model in this polyploid segregation population. We also observed that the relative contribution of individual anthocyanins to the total anthocyanin content varied significantly among different ploid populations, suggesting that genetic background has important impact on the accumulation of the individual anthocyanin compounds. These results will help develop better breeding strategies in a polyploid table grape breeding program for improving the content of anthocyanins, an important class of polyphenolics possessing antioxidant activities and many other health-related benefits.     

Phenotypic segregation and relationships of agronomic traits in Monastrell × Syrah wine grape progeny

The aim of this work was to study the phenotypic segregation of different agronomic and fruit quality traits, and their relationships, in Monastrell × Syrah wine grape progeny. Twenty-two agronomic traits were evaluated and compared for three consecutive years in this progeny. The results show the phenotypic diversity existing in a cross between two different wine grape cultivars. Most of the phenological, productive, morphological, and enological parameters evaluated displayed continuous variation within the progeny, suggesting a polygenic inheritance. Some correlations between traits were detected by the Spearman correlation test, although high coefficients were not found for most of them. Cluster analysis of the progeny grouped the hybrids based on criteria with significance for wine grape breeding. Also, we investigated the relationship between the skin color and total content of anthocyanins with the VvmybA genotype, using the CAPS (Cleaved Amplified Polymorphic Sequence) marker 20D18CB9. The results show that hybrids with two copies of the functional color allele tend to have increased anthocyanins content. Based on this study, 14 genotypes were pre-selected from the breeding population for additional quality studies.     

Intergeneric hybrid between Chrysanthemum × morifolium and Artemisia japonica achieved via embryo rescue shows salt tolerance

Using embryo rescue, we generated an intergeneric hybrid between Chrysanthemum × morifolium ‘Maoyan’ and Artemisia japonica Thunb. Cytological tests confirmed that regenerated plantlets were all genuine hybrids possessing 45 chromosomes, with 27 chromosomes inherited from C. × morifolium (2n = 6x = 54) and the other 18 derived from A. japonica (2n = 4x = 36). Hybrid plant flowered normally. The shape and color of the hybrid flowers and leaves resembled those of chrysanthemum, while leaf width, leaf length, plant height, and inflorescence diameter were intermediate between those of the parents. Hybrid plant had higher levels of chlorophyll and free proline, and lower concentrations of malondialdehyde and Na⁺, than the maternal parent (C. × morifolium), and these levels were correlated with the hybrid’s enhanced salt tolerance. These results clearly demonstrate that intergeneric hybridization is an effective method of cultivar improvement in chrysanthemum.