Factors influencing fruit size in the strawberry (Fragaria ananassa Duch.)

Summary Fruit size is one of the most important characteristics of highly productive strawberry cultivars. The aim of the experiments was to establish the factors responsible for the expression of this trait. The total yield of large fruits correlates closely with the total yield of all fruits and depends mainly on the mean fruit weight of all fruits. The position of fruits on the inflorescence influences the decline of fruit size to a larger extent in small-fruited clones than in the large-fruited ones. The size of the fruit is controlled by the dimension of the receptacle and number of achenes. The stimulating effects of achenes are quite different in various genotypes and the fruit weight per achene declines with the inferior blossom position. The large-fruited clones have bigger leaves, a larger photosynthetic area, and thicker petioles and flower stalks. Their cells are larger, which is common for the giant genotypes. The results suggest that there exists a possibility for indirect selection of fruit size on the basis of some additional parameters, which can be useful particularily in the years of unsuitable weather conditions.     

In vitro selection of strawberry (Fragaria × ananassa Duch.) clones tolerant to salt stress

The method of in vitro selection for increased salt tolerance at the seed germination and early growth phase of strawberry seedlings is proposed. Clone Pau/27 was selected on medium containing 200 mM of NaCl from population obtained by free pollination of cv. ‘Paula2019;. Subsequently, on the same medium 18 salt tolerant clones were attained from the population of seeds collected from self pollinated Pau/27 plants. In the next step we examined the influence of a mild salt stress (75 mM of NaCl) on vegetative growth parameters of selected clones and two cvs.; ‘Paula2019; and ‘Senga Sengana’. All materials in the study on the basis of calculated indexes were divided into four groups differing in reaction to salt. First group (clustered together cv. ‘Paula’, Pau/27 and three second generation clones: Pau/27/11, Pau/27/24, Pau/27/30) represents sensitive genotypes. Second group, including ‘Senga Sengana’, Pau/27/06, Pau/27/10, Pau/27/12, Pau/27/13, Pau/27/15, Pau/27/18, Pau/27/20, Pau/27/21, Pau/27/26, Pau/27/27, Pau/27/31 and Pau/27/32 was designated tolerant. Third group contains only one highly tolerant clone Pau/27/08. The last group comprises two highly sensitive clones (Pau/27/01 and Pau/27/03). This revised version was published online in August 2006 with corrections to the Cover Date.     

A diallel crossing approach aimed on selection for ripening time and yield in breeding of new strawberry (Fragaria × ananassa Duch.) cultivars

The extension of the ripening season in open field production is of high economic interest for strawberry growers. Therefore, targeted breeding for extreme early or late ripening cultivars with high yield potential is of particular interest. Thirteen strawberry cultivars were crossed in a reciprocal way without selfing, and the 144 resulting F₁ populations were evaluated in a field trial over a period of two consecutive years. The data were analysed using a mixed‐model approach adapted for diallel crossing designs using SAS 9.3. The variability in the crossing approach is mainly based on the general combining ability (GCA) of the cultivars (additive effects). Specific and reciprocal combining abilities (non‐additive effects) appear less important. The highest GCAs for the trait Marketable Yield were found for the cultivars ‘Polka’ and ‘Yamaska’. The trait Earliness is bilateral with significantly low GCAs for early ripening in ‘Clery’ and ‘Daroyal’ and significantly high GCAs for late ripening in ‘Yamaska’ and ‘Florence’. Crosses with these cultivars are likely to deliver populations with both high yield and an extended ripening period.     

Comparative QTL mapping for male sterility of cultivated strawberry (Fragaria × ananassa Duch.) using different reference genome sequences

Male sterility is one of the reproductive isolation systems in plants and quite useful for F₁ seed production. We previously identified three independent quantitative trait loci (QTLs) for male sterility of cultivated strawberry, Here, we identified the specific subgenomes in which these QTLs are located by QTL-seq approach. QTLs qMS4.1, qMS4.2, and qMS4.3 were mapped separately in subgenomes Fvb4-4, Fvb4-3, and Fvb4-1, respectively, in ‘Camarosa’ genome assembly v. 1.0.a1. Candidate regions of qMS4.1 and qMS4.3 were clearly detected around 12–26 Mb in Fvb4-4 and 12–14 Mb in Fvb4-1, respectively; those of qMS4.2 were fragmented in Fvb4-3, which suggests that some scaffolds were incorrectly assembled in Fvb4-3. qMS4.3 was mapped to chr4X1 of ‘Reikou’ genome assembly r2.3, and qMS4.1 and qMS4.2 were both mapped to chr4Av, which indicates that differentiation of the subgenomes in which both QTLs are located was insufficient in ‘Reikou’ r2.3. Although ‘Camarosa’ genome assembly v. 1.0.a1 is an unphased map, which merges homologous chromosomes into one sequence, ‘Reikou’ genome assembly r2.3 is a phased map, which separates homologous chromosomes. QTL mapping to different reference genomes clearly showed the specific features of each reference genome, and that using different kinds of reference map could accelerate fine mapping and map-based cloning of certain genes of cultivated strawberry.     

A comparison of genetic relationship measures in strawberry (Fragaria × ananassa Duch.) based on AFLPs, RAPDs, and pedigree data

Nineteen of the major strawberry (Fragaria × ananassa Duch.) cultivars grown in the UnitedStates and Canada were examined for AFLP markerpolymorphisms. For the AFLP reactions, the EcoRI-ACC primer was used in combination with fourMseI primers (MseI-CAC, MseI-CAG,MseI-CAT, or MseI-CTT). Each set ofprimers produced 46–66 scorable fragments ranging insize between 50 and 500 bp. The polymorphic fragmentsproduced from each set of primers were more thansufficient to distinguish among all the cultivars,demonstrating the usefulness of AFLP markers forcultivar identification. Similarity coefficients werecalculated based on data from 228 AFLP markers anddata from 15 previously characterized RAPD markers. The RAPD markers had been specifically selected forfingerprinting purposes because they succesfullydistinguish 41 strawberry cultivars, including the 19cultivars analyzed in this study. Separatedendrograms were constructed based on analysis of theAFLP and RAPD marker data using a neighbor-joiningalgorithm. The dendrograms were compared and found tobe very different. Correlations between similaritycoefficients calculated from AFLP marker data,similarity coefficients calculated from RAPD markerdata, and coefficients of coancestry calculated frompedigree information were evaluated. Interestingly,a better correlation with the coefficients ofcoancestry was observed with the RAPD marker data thanwith the AFLP marker data.     

Development of molecular linkage maps in sweet potato (Ipomoea batatas L.) using sequence‐related amplified polymorphism markers

Sweet potato is an important food crop with high starch content. It is a hexaploid species, for which the chromosomes have not yet been well characterized. In this study, we used 856 SRAP primer pairs to analyse the 240 individuals from a mapping population, which were derived from a hybrid F₁ generation of ‘Luoxushu 8’ (female) and ‘Zhengshu 20’ (male). Genetic linkage maps of the two parents were constructed. In the female parent (‘Luoxushu 8’), the linkage map consisted of 1391 markers, and the length of the linkage map was estimated to be 10,188.4 cM with an average distance of 7.17 cM between markers. In the male parent (‘Zhengshu 20’), the final linkage map consisted of 1,112 markers, and the estimated length of the map was 9,165.17 cM with an average distance of 8.40 cM between markers. Our results provide a basis for the detailed characterization of sweet potato chromosome sequences and the development of related molecular markers.     

Breeding for boron tolerance in lentil (Lens culinaris Medik.) using a high‐throughput phenotypic assay and molecular markers

This study describes the identification of a quantitative trait locus (QTL) in the recombinant inbred line population of ILL2024 × ILL6788 and subsequent validation of associated molecular markers. A high‐quality genetic linkage map was constructed with 758 markers that cover 1,057 cM, with an average intermarker distance of 2 cM. QTL analysis revealed a single genomic region on Lc2 to be associated with B tolerance and accounted for up to 76% of phenotypic variation (Vp). The best markers for B tolerance were assessed for their utility in routine breeding applications using validation panels of diverse lentil germplasm and breeding material derived from ILL2024. A marker generated from the dense genetic map of this study was found to be the most accurate of all markers available for B tolerance in lentil, with a success rate of 93% within a large breeding pool derived from ILL2024. However, given the number of the unrelated lines for which the marker–trait association was not conserved, B tolerance screening is still required at later stages to confirm predicted phenotypes.     

Construction of high‐throughput genotyped chromosome segment substitution lines in rice (Oryza sativa L.) and QTL mapping for heading date

Chromosome segment substitution lines (CSSLs) provide ideal materials for quantitative trait loci (QTLs) mapping and genetic dissection of complex traits. In this study, we developed a set of CSSL population consisting of 175 lines, which were derived between the recipient ‘Guangluai 4’ and the donor ‘Nipponbare’. Based on 260 molecular markers, we firstly constructed a physical map of core 97 lines. Then, these 97 lines were further genotyped based on resequencing data, and a resequencing‐based physical map was constructed. Compared with the molecular marker‐based physical map, the resequencing‐based physical map of 97 lines contained 367 substituted segments with 252 newly discovered segments. The total size of the 367 substituted segments was 1,074 Mb, which was 2.81 times the size of rice genome. Using the 97 CSSLs as materials, we identified nine QTLs for heading date and three of them were firstly reported. All the QTLs had positive additive effects, ranging from 9.50 to 16.50 days. These CSSLs may greatly help forge a new resource for functional genomics studies and molecular breeding in rice.     

Identification of incompatibility genotypes in almond (Prunus dulcis Mill.) using specific primers based on the introns of the S-alleles

Identification of the incompatibility genotypes of almond cultivars is important in breeding programmes for designing crosses and for selecting progeny. This paper describes a novel molecular technique for the identification of S‐alleles in almond based on the use of PCR primers designed from the sequences of the introns without the need for restriction enzyme digestion. Nine specific pairs of primers have been designed for the S1, S2, S5, S7, S8, S9, S10 (putative), S23 and Sf alleles, and these confirmed the S‐allele specificities for 22 of the 23 accessions for which published information is available. This technique provides a precise method for identifying S‐alleles from the genomic DNAs of almond cultivars, and will be useful for confirming the segregation of alleles in breeding progeny.     

Evaluation of the Ph‐3 gene‐specific marker developed for marker‐assisted selection of late blight‐resistant tomato

Late blight caused by Phytophthora infestans is one of the most destructive diseases of tomato (Solanum lycopersicum L.) that mainly occurs in cool and wet environments. With the spread of the A2 mating type and new clonal lineages, fewer fungicides provide effective control of the disease, which has increased its worldwide threat. Host resistance could contribute significantly to sustainable disease control. Ph‐3 is a race‐specific late blight resistance gene commonly used in commercial tomato breeding. Availability of precise and easy to use gene‐based markers would facilitate selection. In this study, a Ph‐3 on‐gene cleaved amplified polymorphic sequence (CAPS) marker, Ph3.gsm/HincII, was developed based on the published gene sequence of Ph‐3. The effectiveness of the marker was evaluated along with other published Ph‐3 markers using an F₉ recombinant inbred line (RIL) population derived from NC 23E‐2(93) × L3708. Markers Ph3.gsm/HincII and TG328/BstNI accurately genotyped the RIL population for Ph‐3. In addition, Ph3.gsm/HincII was able to differentiate variable susceptible alleles. This reliable codominant DNA marker would be very useful in marker‐assisted selection, particularly for resistance gene pyramiding.     

Identification and marker‐assisted introgression of QTL conferring resistance to bacterial leaf blight in cowpea (Vigna unguiculata (L.) Walp.)

Bacterial leaf blight (BLB), caused by Xanthomonas axonopodis pv. vignicola (Xav), is widespread in major cowpea [Vigna unguiculata (L.) Walp.] growing regions of the world. Considering the resource poor nature of cowpea farmers, development and introduction of cultivars resistant to the disease is the best option. Identification of DNA markers and marker‐assisted selection will increase precision of breeding for resistance to diseases like bacterial leaf blight. Hence, an attempt was made to detect QTL for resistance to BLB using 194 F_2 : 3 progeny derived from the cross ‘C‐152’ (susceptible parent) × ‘V‐16’ (resistant parent). These progeny were screened for resistance to bacterial blight by the leaf inoculation method. Platykurtic distribution of per cent disease index scores indicated quantitative inheritance of resistance to bacterial leaf blight. A genetic map with 96 markers (79 SSR and 17 CISP) constructed from the 194 F₂ individuals was used to perform QTL analysis. Out of three major QTL identified, one was on LG 8 (qtlblb‐1) and two on LG 11 (qtlblb‐2 and qtlblb‐3). The PCR product generated by the primer VuMt337 encoded for RIN2‐like mRNA that positively regulate RPM1‐ and RPS2‐dependent hypersensitive response. The QTL qtlblb‐1 explained 30.58% phenotypic variation followed by qtlblb‐2 and qtlblb‐3 with 10.77% and 10.63%, respectively. The major QTL region on LG 8 was introgressed from cultivar V‐16 into the bacterial leaf blight susceptible variety C‐152 through marker‐assisted backcrossing (MABC).     

Allelic polymorphism and inheritance of MdACS1 and MdACO1 genes in apple (Malus × domestica Borkh.)

The allelic polymorphism and inheritance of MdACS1 and MdACO1 genes were analysed in 28 apple cultivars, which were derived from reciprocal crosses of the following parental pairs: ‘Golden Delicious’ × ‘James Grieve’, ‘Golden Delicious’ × ‘Jonathan’, ‘Cox's Orange Pippin’ × ‘Golden Delicious’, ‘Cox's Orange Pippin’ × ‘Jonathan’. Polymorphisms were detected by PCR and the use of two restriction enzymes (BamH1 and RsaI). In addition, new primers were designed for the further discrimination of MdACO1 alleles. Two alleles of MdACS1 gene (MdACS1‐1 and MdACS1‐2) and three alleles of MdACO1 gene (a, b and c) were detected. Cloning and sequencing of MdACO1 alleles confirmed a high conservation and some differences within the coding regions and helped to reconcile between different numbering systems. Observed segregations confirmed that alleles a, b and c belonged to the MdACO1 gene. It is apparent that polymorphisms within the MdACS1 and MdACO1 genes could aid cultivar genotyping and identification and, furthermore, that the MdACS1‐2/2 genotype is correlated with a long apple storage life.     

The effect of the Waxy locus (Granule Bound Starch Synthase) on pasting curve characteristics in specialty rices (Oryza sativa L.)

Starch structure and functionality have a significant impact on the utilization of cereal grains as food and feed. Starch viscosity characteristics are used to characterize rice cooking, processing and eating quality. In order to examine the genetics of viscosity characteristics, we developed molecular markers for five of the major enzymes involved in starch synthesis in the endosperm: granule bound starch synthase, soluble starch synthase, rice branching enzymes 1 and 3 and starch debranching enzyme. These markers were polymorphic in a cross between specialty rice varieties of diverging amylose content and viscosity characteristics. Our results indicate that the Waxy locus, encoding the gene for granule bound starch synthase, has a significant effect on peak viscosity, hot paste viscosity, cool paste viscosity, breakdown and setback viscosity. We estimate that the tightly linked (5–10 cm)locus for starch synthase may have a lesser, additive effect. This revised version was published online in July 2006 with corrections to the Cover Date.     

Development of a molecular marker for self‐compatible S4′ haplotype in sweet cherry (Prunus avium L.) using high‐resolution melting

Sweet cherry (Prunus avium L.) has stylar gametophytic self‐incompatibility, which is controlled by the multi‐allelic S‐locus and encompasses the highly polymorphic genes for the S‐ribonuclease (S‐RNase) and S‐haplotype‐specific F‐box (SFB), which are female and male determinants, respectively. The self‐compatible mutant SFB4′ corresponds to an allele variant of SFB4 and presents a frameshift mutation. Even though male‐determinant molecular markers can discriminate between SFB4 and SFB4′ alleles, the methods required are laborious, time‐consuming and expensive, and not suitable for massive analysis and integration into breeding programmes. Our aim was to develop molecular markers for the evaluation of self‐compatibility alleles in sweet cherry, that could be used as a high‐throughput screening strategy to identify SFB4 and SFB4′ alleles, based on a marker for male determinacy. Our results were consistent using primers flanking the mutation responsible for the SFB4′ allele. We designed a specific molecular marker and confirmed it in sweet cherry commercial varieties. This new molecular marker is feasible for self‐compatibility alleles in the male determinant in sweet cherry‐assisted breeding programs.     

Identification of QTLs controlling low‐temperature tolerance during the germination stage in cucumber (Cucumis sativus L.)

Poor seed germination of cucumber at suboptimal temperatures is a great concern for growers wishing to take advantage of the early market. The development of low‐temperature‐tolerant varieties would be aided by understanding the inheritance of the trait and mapping its locus. In this study, a set of 140 recombinant inbred lines (RILs) derived from a cross between 65G (low‐temperature‐tolerant) and 02245 (low‐temperature‐sensitive) was used to identify the QTLs linked with low‐temperature tolerance. A linkage map was developed using 135 simple sequence repeat (SSR) markers and five insertion–deletion (Indel) markers, and three QTLs were identified, qLTG1.1, qLTG2.1 and qLTG4.1. qLTG1.1, the major one for germination rate, germination energy and germination index, explained more than 50% of the observed phenotypic variability. The major QTL for radicle length, qLTG4.1, explained 13.8% of the phenotypic variability. The results showed that qLTG1.1 and qLTG4.1 play an important role in low‐temperature tolerance during seed germination of cucumber and provide a basis for further fine mapping to determine the molecular mechanism for this trait.