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.     

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.     

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.     

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).     

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.     

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.     

Inheritance of sugar and acid contents in the ripe berries of a tetraploid × diploid grape cross population

Pearl millet [Pennisetum glaucum (L.) R. Br.] is a major warm-season cereal, grown primarily for grain production in the arid and semi-arid tropical regions of Asia and Africa. Iron (Fe) and zinc (Zn) deficiencies have been reported to be a food-related primary health problem affecting nearly two billion people worldwide. Improving Fe and Zn densities of staple crops by breeding offers a cost-effective and sustainable solution to reducing micronutrient malnutrition in resource poor communities. An understanding of the genetics of these micronutrients can help to accelerate the breeding process, but little is known about the genetics and heterosis pattern of Fe and Zn densities in pearl millet. In the present study, ten inbred lines and their full diallel crosses were used to study the nature of gene action and heterosis for these micronutrients. The general combining ability (GCA) effects of parents and specific combining ability (SCA) effects of hybrids showed significant differences for both of the micronutrients. However, the predictability ratio (2σ²gca/(2σ²gca + σ²sca)) was around unity both for Fe and Zn densities, implying preponderance of additive gene action. Further, highly significant positive correlation between mid-parent values and hybrid performance, and no correlation between mid-parent values and mid-parent heterosis confirmed again the predominant role of additive gene action for these micronutrients. Barring a few exceptions with one parent, hybrids did not outperform the parents having high Fe and Zn levels. This showed that there would be little opportunity, if any, to exploit heterosis for these mineral micronutrients in pearl millet. In general, high Fe and Zn levels in both of the parental lines would be required to increase the probability of breeding high Fe and Zn hybrids.     

Long-term trends and genetic architecture of seed characteristics,grain yield and correlated agronomic traits in triticale (×Triticosecale Wittmack)

The aim of this study was to investigate long-term genetic trends and the genetic architecture of grain yield, seed characteristics and correlated agronomic traits in triticale. Therefore, a panel of 846 diverse triticale genotypes was assessed for three agronomic and three seed shape- and size-related traits. We observed a high genotypic variation and a high heritability for all traits. Analysing the development of these traits during the last decades revealed a continuous increase for grain yield and thousand-kernel weight, and a slight increase in seed width. The seed characteristics and thousand-kernel weight formed a complex of highly positive correlated traits. Genome-wide association mapping revealed many small-effect QTL and a few moderate-effect QTL. The allele frequencies of the moderate-effect QTL followed the same temporal trends as observed for the phenotype. In line with the phenotypic correlations, we identified several pleiotropic QTL for grain yield, thousand-kernel weight, seed width and seed area. Our results illustrate the continuous progress achieved in triticale breeding and suggest that triticale seeds have been selected to be more spherical in modern cultivars.     

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.     

Detection of downy and powdery mildew resistance QTL in a ‘Regent’ × ‘RedGlobe’ population

One hundred and eighty six F₁ plants from a ‘Regent’ × ‘RedGlobe’ cross were used to generate a partial linkage map with 139 microsatellite markers spanning all 19 chromosomes. Phenotypic scores for downy mildew, taken over two years, confirmed a major resistance QTL (Rpv3) against downy mildew in the interval VVIN16-cjvh to UDV108 on chromosome 18 of ‘Regent’. This locus explained up to 62 % of the phenotypic variance observed. Additionally a putative minor downy mildew resistance locus was observed on chromosome 1 in one season. A major resistance locus against powdery mildew (Ren3) was also identified on chromosome 15 of ‘Regent’ in the interval UDV116 to VChr15CenGen06. This study established the efficacy of and validated the ‘Regent’-derived downy and powdery mildew major resistance genes/QTL under South African conditions. Closely linked SSR markers for marker-assisted selection and gene pyramiding strategies were identified.     

Phenotypic correlations, G × E interactions and broad sense heritability analysis of grain and flour quality characteristics in high latitude spring bread wheats from Kazakhstan and Siberia

Grain and flour samples of 42 high latitude spring bread wheat genotypes from Kazakhstan and Siberia evaluated in a multi-location trial were analyzed for grain concentrations of protein, zinc (Zn) and iron (Fe), as well as flour quality characteristics. The genotypes showed high grain protein concentrations (14–19%), but low dough strength was a common feature for most of them. Significant positive correlations were found between grain protein and flour protein, gluten, gliadin, gli/glu ratio, Zn, and Fe contents. Grain protein was also correlated positively with hardness, sedimentation, farinograph dough development time (DDT), stability time and ash content. Grain Fe concentration was positively associated with sedimentation, stability time, water absorption and valorimeter value, suggesting that improvements in micronutrient concentrations in the grain parallels enhancement in gluten strength. Interestingly, glutenin content correlated negatively with the concentrations of grain and flour protein, gluten, and minerals; and also with gluten deformation index (IDK), DDT, and stability time. Conversely, gliadin content showed strong positive correlations with the concentrations of grain and flour protein, gluten, and minerals. Gliadin also correlated positively, but in lesser magnitude, with DDT, stability time and IDK. Environment and G×E interaction were important sources of variation for some quality characteristics. This was reflected in the low broad sense heritability (H) values for traits related to flour strength, such as sedimentation, IDK, stability time and gliadin content. Breeding strategies, including three testing locations at the advanced selection stages, are adequate for the enhancement of most of the quality traits, but faster improvement in flour strength could be achieved with a larger number of locations.     

Unreduced 3x gamete formation of allotriploid hybrid derived from the cross of Primula denticulata (4x)?×?P. rosea (2x) as a causal factor for producing pentaploid hybrids in the backcross with pollen of tetraploid P. denticulata

A triploid hybrid, which was obtained from interspecific crosses between tetraploid Primula denticulata (2n = 4x = 44) and P. rosea (2n = 2x = 22), successfully produced 11 plants by backcrossing with pollen of tetraploid P. denticulata. Analysis of ploidy level using flow cytometry and chromosome counting in the 11 BC₁ plants revealed that all progeny had much larger DNA contents and chromosome number than both parents. In this triploid-tetraploid (3x–4x) crossing, progeny was predominantly true or near pentaploid presumably produced by the fertilization between true or near triploid female gamete produced from triploid hybrid and diploid pollen of tetraploid P. denticulata. These results suggest that unreduced (3x) or near triploid female gametes were partially produced by single step meiosis, either first-division restitution or second-division restitution process. The zygotes formed by the fertilization between true or near triploid egg produced by single step meiosis in triploid hybrid and diploid pollen produced by normal meiosis of tetraploid P. denticulata might be the only survivors in embryogenesis.     

QTL mapping in diploid potato by using selfed progenies of the cross <Emphasis Type="Italic">S. tuberosum</Emphasis> × <Emphasis Type="Italic">S. chacoense</Emphasis>

Usually, mapping studies in potato are performed with segregating populations from crosses between highly heterozygous diploid or tetraploid parents. These studies are hampered by a high level of genetic background noise due to the numerous segregating alleles, with a maximum of eight per locus. In the present study, we aimed to increase the mapping efficiency by using progenies from diploid inbred populations in which at most two alleles segregate. Selfed progenies were generated from a cross between S. tuberosum (D2; a highly heterozygous diploid) and S. chacoense (DS; a homozygous diploid clone) containing the self-incompatibility overcoming S locus inhibitor (Sli-gene). The Sli-gene enables self-pollination and the generation of selfed progenies. One F2 population was used to map several quality traits, such as tuber shape, flesh and skin color. Quantitative trait loci were identified for almost all traits under investigation. The identified loci partially coincided with known mapped loci and partially identified new loci. Nine F3 populations were used to validate the QTLs and monitor the overall increase in the homozygosity level.     

Quantitative trait loci analysis of citrus leprosis resistance in an interspecific backcross family of (<Emphasis Type="Italic">Citrus reticulata</Emphasis> Blanco × <Emphasis Type="Italic">C. sinensis</Emphasis> L. Osbeck) × <Emphasis Type="Italic">C. sinensis</Emphasis> L. Osb

Leprosis, caused by citrus leprosis virus (CiLV) and transmitted by the tenuipalpid mite Brevipalpus phoenicis, is one of the most important viruses of citrus in the Americas. Sweet oranges (Citrus sinensis L. Osb.) are highly susceptible to CiLV, while mandarins (C. reticulata Blanco) and some of their hybrids have higher tolerance or resistance to this disease. The mechanisms involved in the resistance and its inheritance are still largely unknown. To study the quantitative trait loci (QTL; quantitative trait loci) associated with the resistance to CiLV, progeny analyses were established with 143 hybrid individuals of ‘Pêra’ sweet orange (C. sinensis L. Osb.) and ‘Murcott’ tangor (C. reticulata Blanco × C. sinensis L. Osb.) from controlled crossings. Disease assessment of the hybrid individuals was conducted by infesting the plants with viruliferous mites in the field. The experiment consisted of a randomized completely block design with ten replicates. The evaluated phenotypic traits were incidence and severity of the disease on leaves and branches, for a period of 3 years. The MapQTL™ v.4.0 software was used for the identification and location of possible QTL associated with resistance to CiLV on a genetic map obtained from 260 AFLP and 5 RAPD markers. Only consistent QTLs from different phenotypic traits and years of evaluation, with the critical LOD scores to determine the presence or absence of each QTL calculated through the random permutation test, were considered. A QTL was observed and had a significant effect on the phenotypic variation, ranging from 79.4 to 84% depending on which trait (incidence or severity) was assessed. This suggests that few genes are involved in the genetic resistance of citrus to CiLV.