Quantitative trait loci of acid detergent fiber and grain chemical composition in hulled × hull-less barley population

Cultivated barley is the major livestock feed grain in the Northern Plains and Northwestern United States due to the fact that its short growing season and limited rainfall limit the planting and production of corn. Starch and fiber content play a significant role in feedlot performance of animals raised on barley feed. To study the underlying genetic locations and mechanisms for these traits, a recombinant inbred line population was derived from a cross between the hulled barley cultivar Valier and a hull-less Swiss landrace line, PI370970. Valier has a high acid detergent fiber content (ADF) and low starch and protein while PI370970 contains low ADF and high starch and protein content. To detect associated QTLs, data were collected and analyzed from irrigated and rain-fed environments. A total of 30 main effect QTLs and four epistatic QTLs were identified which conditioned ADF, starch and protein content under rain-fed, irrigated and combined analyses. These QTLs were located on chromosomes 2H, 3H, 5H, 6H and 7H. Major ADF and starch QTL were identified on chromosome 7H near the nud locus (the locus controlling hulled vs. hull-less caryopsis). High heritability estimates for both ADF and starch content suggest that early selection for these traits during breeding would be productive. Low ADF-QTL were independently verified in a second population in a different genetic background.     

Mapping quantitative trait loci (QTL) for grain size in rice using a RIL population from Basmati × indica cross showing high segregation distortion

Grain size is one of the three productivity related traits in rice and hence a major target for genetic improvement. Since understanding genetic variation in grain size between Basmati and indica genotypes is important for rice improvement, a recombinant inbred population was developed from a traditional aromatic cultivar ‘Basmati 370’ and a non-aromatic indica genotype ‘IRBB60’. This population was phenotyped in two locations for grain length (GL), grain breadth (GB), GL/GB ratio (LBR) and grain weight (GW). Though the RIL population reported in the current study exhibited segregation distortion (SD) for 54 % of the markers, they were utilized in analysis using an appropriate statistical package, PROC QTL in the SAS environment. Interval mapping revealed a total of 15 QTLs for GL, seven for GB, 15 for LBR and two for GW. Among them 13 were not reported earlier and thus novel. For a known major QTL identified in the study, GW8 for GB, a PCR based functional marker was designed and validated. This is the first report wherein a very high proportion of markers (>50 %) exhibiting SD have been successfully used for QTL mapping.     

Molecular mapping of quantitative trait loci for domestication traits and β-glucan content in a wheat recombinant inbred line population

Genetic maps are useful for analysis of quantitative trait loci (QTLs) and for marker-assisted selection (MAS) in breeding. A simple sequence repeat (SSR) marker linkage map of common wheat was constructed based on recombination inbred lines (RILs) derived from a cross between Chinese Spring and spelt wheat. The map included 264 loci on all wheat chromosomes covering 2,345.2 cM with 962, 794.6, and 588.6 cM for the A, B, and D genomes, respectively. Using the RILs and the map, we detected 42 putative QTLs on 15 chromosomes for ear length, spikelet number, spike compactness, kernel length, kernel width, kernel height and β-glucan content. Each QTL explained 4–45% of the phenotypic variation. Five QTL cluster regions were detected on chromosomes 1A, 5AL, 2B, 2D, and 4D. The first QTLs for β-glucan content in wheat were identified on chromosomes 3A, 1B, 5B, and 6D.     

Advanced-backcross QTL analysis in spring barley: IV. Localization of QTL × nitrogen interaction effects for yield-related traits

The advanced backcross quantitative trait locus (AB-QTL) analysis has proven its usefulness to identify and localize favourable alleles from exotic germplasm and to transfer those alleles into elite varieties. In a balanced design with up to six environments and two nitrogen fertilization (N treatment) levels, a 4-factorial mixed model analysis of variance (ANOVA) was used to identify QTL main effects, QTL × environment interaction effects and QTL × N treatment interaction effects in the spring barley BC₂DH population S42. The yield-related traits studied were number of ears per m², days until heading, plant height, thousand grain weight (TGW) and grain yield. In total, 82 QTLs were detected for all traits. This finding was compared to a previous QTL study of the same population S42, where the current field data was reduced to one half through restriction of the analysis to the standard N treatment level (von Korff et al., Theor Appl Genet 112: 1221–1231, 2006). These authors located 54 QTLs for the same traits by applying a 3-factorial mixed model similar to the current model but excluding the factor N treatment. We found that QTL × environment interaction, alone or in combination, accounted for 24 of the newly uncovered QTLs, whereas QTL × N treatment interaction was of lesser importance with six new cases in total. A valuable QTL interacting with N treatment has been identified on chromosome 7H where lines carrying the wild barley allele were superior in number of ears per m² in either N treatment. We conclude that in population S42 the extension of the phenotype data set and the inclusion of N treatment into the mixed model increased the power of QTL detection by providing an additional replication rather than by revealing specific N treatment QTLs.     

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.     

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.     

Quantitative trait locus mapping for Verticillium wilt resistance in a backcross inbred line population of cotton (Gossypium hirsutum × Gossypium barbadense) based on RGA-AFLP analysis

Verticillium wilt (VW), caused by Verticillium dahliae Kleb., is one of the most important diseases in cotton. The objective of this study was to map quantitative trait loci (QTLs) conferring VW resistance using resistance gene analog (RGA)-targeted amplified fragment length polymorphism (RGA-AFLP) markers in an interspecific backcross inbred line mapping population, consisting of 146 lines from a susceptible Sure-Grow 747 (Gossypium hirsutum L.) × resistant Pima S-7 (G. barbadense L.) cross. VW resistance was evaluated in replicated tests based on disease incidence in the field, and disease incidence and severity in the greenhouse. Of 160 polymorphic RGA-AFLP markers, 42 were significantly correlated with one or more VW traits and 41 were placed on a linkage map which covered 1,226 cM of the cotton genome and contained 251 other molecular markers. Three QTLs for VW resistance were detected, each of which explained 12.0–18.6 % of the phenotypic variation. Two of these QTLs for disease incidence and severity detected in the greenhouse inoculation tests using root wounding are located on chromosome c4. Both are closely linked to four RGA-AFLP markers and therefore considered as the same QTL for VW resistance. The other QTL detected in the field test was located on c19 and flanked by several RGA-AFLP markers. The desirable QTL allele on c4 for VW resistance detected in the greenhouse was from the VW susceptible Upland parent and absent from the resistant Pima parent which was more VW susceptible due to the disarmament of the first line of defense mechanism due to root wounding during inoculation. The other desirable VW resistance QTL allele, on c19, was from the resistant parent Pima S-7, consistent with the fact that Pima cotton was more resistant to VW when naturally infected in the field. The results should facilitate the development of more sequence specific markers and the transfer of VW resistance from Pima to Upland cotton through marker-assisted selection.     

Quantitative trait loci associated with lodging tolerance in soybean cultivar ‘Toyoharuka’

Lodging tolerance (LT) is an important trait for high yield and combine-harvesting efficiency in soybean [Glycine max (L.) Merr.]. Many previous studies have investigated quantitative trait loci (QTLs) for lodging score (LS) in soybean. Most of the investigated QTLs were located in the proximal region of maturity or growth habit loci. The aim of this study was to identify genetic factors for LT not associated with maturity or growth habit. QTL analysis was performed using a recombinant inbred line (RIL) population derived from a cross between ‘Toyoharuka’ (TH), a lodging-tolerant cultivar, and ‘Toyomusume’ (TM). The genotypes of TH and TM were estimated as both e1e2E3E4 and dt1. The average LS over 4 years was used for QTL analysis, identifying a major and stable QTL, qLS19-1, on chromosome 19. The LS of the near-isogenic line (NIL) with the TH allele at Sat_099, the nearest marker to qLS19-1, was significantly lower than the NIL with the TM allele at that position. The TH allele at Sat_099 rarely had a negative influence on seed yield or other agronomic traits in both NILs and the TM-backcrossed lines. Our results suggest that marker-assisted selection for qLS19-1 is effective for improving LT in breeding programs.     

Identification of quantitative trait loci for seed storability in rice (Oryza sativa L.)

In the present study, quantitative trait loci (QTLs) controlling seed storability based on relative germination rate (%) were dissected using a saturated linkage map and a recombinant inbred lines (RILs) derived from a cross of japonica cultivar Asominori (Oryza sativa L.) and indica cultivar IR24 (Oryza sativa L.). A total of three QTLs (qRGR-1, qRGR-3 and qRGR-9) were detected on chromosomes 1, 3 and 9 with LOD score ranging from 3.45 to 6.95 and the phenotypic variance explained from 16.72% to 28.63%. The IR24 alleles were all associated with seed storability at all the three QTLs. The existence of these QTLs was confirmed using IR24 chromosome segment substitution lines (CSSLs) in Asominori genetic background (AIS). By QTL comparative analysis, the QTL, qRGR-9 on chromosomes 9 appeared to be consistent with another rice population, this region may provide an important region for isolating this responsible gene. These results also provide the possibilities of enhancing Seed storability in rice breeding program by marker-assisted selection (MAS) and pyramiding QTLs. Y. Xue and S. Q. Zhang—joint first authors.     

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.     

Assessing the importance of genotype × environment interaction for root traits in rice using a mapping population III: QTL analysis by mixed models

The phenotypic analysis of field experiments includes information about the experimental design, the randomization structure and a number of putative dependencies of environment and design factors on the trait investigated. In QTL studies, the genetic correlation across environments, which arises when the same set of lines is tested in multiple environments, plays an important role. This paper investigates the effect of model choice on the set and magnitude of detected root QTL in rice. Published studies on QTLs for root traits indicate that different results are obtained if varying genetic populations are used and also if different environmental conditions are included. An experiment was conducted with 168 RILs of the Bala × Azucena mapping population plus parents as checks under four environmental conditions (low light, low nitrogen, drought and a control environment). We propose a model that incorporates all relevant experimental information into a composite interval mapping approach based on a mixed model, which especially considers the correlation of genotypes in different environments. An extensive sequential model selection procedure was applied based on the phenotypic model, using the AIC to determine an appropriate random structure and Type 3 Wald F-tests for selection of fixed effects. In a first step we checked whether any of the fixed effects and random (nested) design effects could be dropped. Secondly, an appropriate covariance structure was chosen for genotype × environment interaction. In a third step Box-Cox transformations were applied based on residual analysis. We compared profiles of composite interval mapping scans with and without the inclusion of genotype × environment interaction and the experimental design information. Some distinct differences in profiles indicate that insufficient modeling of the non-QTL part can lead to an overly optimistic interpretation of QTL main effects in interval mapping. It is concluded that mixed model QTL mapping offers a reasonable way to separate environmental and genetic influences in the evaluation of quantitative genes and especially enables a more realistic assessment of QTL and QTL × environment effects than standard approaches by including all relevant effects.     

Phenotypic diversity and relationships of fruit quality traits in inter-specific almond × peach backcrosses breeding progenies

Nineteen agrochemical traits of 20 almond inter-specific backcrosses progenies were evaluated and compared for three consequence years to find out their phenotypic diversity and determine the relationships of fruit quality traits in almond × peach backcrosses breeding progenies. The variation was observed for traits of phenology parameters (blooming time, ripening time), Physical parameters (fruit weight, width, height, shape, thickness, skin pubescences, colour and flower type), chemical parameters (total sugar content, soluble solids content and acidity) and sensory parameters (attractiveness, taste, and flavor) and yield. Many fruit characteristics that are important to breeders are present in this collection. A high variability was found in the evaluated almond progenies and significant differences were found among them in all studied quality attributes. Year-by-year variations were observed for majority of traits. A significant correlation was found among the fruit height, fruit width, skin pubescences and yield. Fruit height showed a significant positive correlation with fruit weight and fruit thickness and some other traits and a negative correlation with the titratable acidity, skin pubescences and fruit flavour. A high negative correlation was found between the fruit weight and titratable acidity (?0.8). Low coefficients were got between the flower colour and skin pubescences. In addition, principal component analysis it possible to established similar groups of genotypes depending on their quality characteristics and to study relationships among pomological traits in almond progenies evaluated.     

Variation for agronomic and processing traits in Solanum tuberosum haploids × wild species hybrids

Summary The broad range of wild and cultivated species relatives of the commerical potato (Solanum tuberosum L.), guarantees the existence of a gene reservoir to be screened for traits that are absent or present only in low frequencies in the cultivated germplasm. Haploids (2n=2x=24) extracted from the cultivated tetraploid (2n=4x=48) germplasm cross easily with diploid (2n=2x=24) potato species and produce fertile progeny. As most haploid × species hybrids tuberize under long day conditions they can be maintained clonally and evaluated for the traits of interest. Three populations involving Tuberosum haploids × Solanum bukasovii (tub x buk), Tuberosum haploids × Solanum sparsipilum, (tub × spl) and Tuberosum haploids × Solanum berthaultii (tub x ber) clones, were planted at two locations in Wisconsin. The haploids were derived from W231, a selected clone from the University of Wisconsin Potato Breeding Program. The objectives were: to evaluate the H-S populations for agronomic and processing traits, and to determine the phenotypic associations between them. Data were recorded on haulm maturity (HM), tuber weight (TW) and tuber number (NT) per plant, specific gravity (SG), chip color after harvest (CH), and chip color after storage at 4° C and one week of reconditioning at room temperature (CH1). Results for SG and CH indicated good potential of the germplasm evaluated to introgress these traits into the commercial potatoes. For instance, the SG mean for tub x buk, tub x spl and tub x ber were 1.079, 1.086 and 1.082, respectively, and their means for CH were 4.8, 3.9 and 3.5. Chip color after storage and reconditioning was found in low frequency in the populations. Four clones in the tub x spl population, and three clones in the tub x ber population had CH1 4.0, the commercially acceptable score for this trait. Significant (p 0.01) phenotypic correlations (r) were found between HM and SG (r=–0.46 in tub x buk, r=–0.61 in tub x spl, and r=–0.34 in tub x ber), NT and TW (r=0.79 in tub x buk, r=0.88 in tub x spl, and r=0.71 in tub x ber), and TW and SG (r=0.40 in tub x buk, and r=0.36 in tub x spl). The correlation coefficients between processing traits were not significant, which may indicate the presence of separate genetic mechanisms governing the inheritance of these traits.     

Segregation and associations of enological and agronomic traits in Graciano × Tempranillo wine grape progeny (Vitis vinifera L.)

The main objective of this research was the evaluation of the variability present in a segregating wine grape population derived from a cross between Graciano × Tempranillo, two Spanish varieties, in order to select improved genotypes with potential for producing high-quality wines in a climate change scenario. For that purpose, the phenotypic segregation of 16 agronomic traits related to production and phenology and 11 enological traits related to technical and phenolic maturity was studied in the progeny for three consecutive years. All traits presented transgressive segregation and continuous variation. Year effect was significant for all traits except total, extractable and skin anthocyanins content. However, a high level of genotype consistency for enological traits was revealed by repeatabilities and correlations between years. Significant correlations among traits were observed but most associations were weak. Furthermore, the CAPS (Cleaved Amplified Polymorphic Sequence) marker for the VvmybA genotype was tested to determine whether it would be useful in indirect selection for berry anthocyanins content. The results showed that the number of homozygous and heterozygous genotypes for the functional colour allele adjusted to a 1:1 segregation ratio, and that homozygous genotypes had significantly higher anthocyanins content. Principal component analysis found eight variables that contributed up to 80 % of the phenotypic variability present in the population. Seven groups of hybrids were distinguished based on ripening time, cluster weight, berry weight and anthocyanins content by cluster analysis; and fourteen genotypes were pre-selected for further research.     

Genetic control of pre-heading phases in the Steptoe × Morex barley population under different conditions of photoperiod and temperature

Although there are numerous studies on the genetic control of flowering time in barley, little is known on the genetic control of duration of different particular pre-heading phases. Extending the stem elongation phase (SE), without modifying total time to heading, has been proposed as a trait to raise yield potential. Moreover, studying the genetic control of pre-heading phases would be of interest for a better understanding of crop phenology which is crucial for adaptation. We studied the genetic control of the leaf and spikelet intitiation phase (LS), the stem elongation phase, and within this, from the onset of jointing to flag leaf (J-FL), and from then to heading (FL-HD), in the Steptoe × Morex population, which is known to segregate for some major developmental genes, under different environmental conditions. After a preliminary greenhouse study in which the appropriateness of the population was tested, 130 double haploid lines and the two parents were grown under four field environments that differed in photoperiod and temperature conditions. Amongst all QTLs detected (13), only three were significant for HD and for both LS and SE and with the same allele direction (although with greater effects in one phase than the other in some cases). Genotype by environment interactions for LS and HD were due to both photoperiod and other factors as temperature or its interaction with photoperiod, while for SE responses to only photoperiod were negligible. QTL × E interactions were important for some QTLs, and either cross-over (e.g. Ppd-H1) or quantitative (e.g. Ppd-H2). However, heritability across field environments for the ratio SE/LS was high (0.8) and several of the QTL effects that were significant for only LS or SE, were conserved across different environments, that is, they were significant with the increasing allele derived from the same parent in all or most environments.     

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.