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We investigated the potential of markers associated with floral traits for parental selection in a cut rose breeding program. We analysed six Kompetitive Allele Specific PCR (KASP) markers for three important floral traits, petal length, petal number and scent, derived from experiments in a garden rose population. The six markers were applied to genotype a collection of 384 parental genotypes used for commercial cut rose breeding. We phenotyped a selection of progeny derived from pairs of parents having either high or low dosages of (contrasting) marker alleles associated with these traits. Significant differences were found between the contrasting progeny groups for each of the traits, although parents with the optimal allele dosage combinations could not always be used for the crosses. This not only supports the robustness of these marker‒trait associations but also demonstrates their potential for commercial rose breeding. It also demonstrates the use of marker information generated in garden rose populations for cut rose breeding. [ABSTRACT FROM AUTHOR]

The panicle erectness (PE) japonica cultivars have been widely planted in China. However, the relatively low yield level per plant and inferior eating and cooking quality of PE japonica cultivars are needed to improve further. In present study, a typical PE japonica cultivar, Nanjing 46, was selected as target for improving yield and grain quality by the way of introgression of Gn1a, qPC-1, and sd1 allele conferring grain number, grain protein content (GPC), and plant height, respectively. We obtained the improved lines containing Gn1a, qPC-1-sd1, and qPC-1-sd1-Gn1a through consecutive backcrossing with the help of gene-tagged markers. Agronomic and quality trait analysis showed that the introgression of Gn1a allele exhibited a positive effect on many panicle characters, including longer panicle length and grain length, more grain numbers per panicle, finally resulting in an increased grain yield. The introgression of sd1 allele could significantly reduce the plant height, and no negative effects were found on the panicle performance of the plants containing Gn1a allele. The introgression of qPC-1 could significantly reduce GPC, then increase rice palatability based on the RVA analysis. The result indicated that it is feasible to improve rice yield and grain quality of PE japonica cultivars by replacing these three favorable alleles simultaneously. This strategy could also be applied in the improvement of common japonica cultivars. [ABSTRACT FROM AUTHOR]

Flowering time is crucial in watermelon (Citrullus lanatus) production as it determines time of fruit set. Early flowering is desirable because it enables crops to escape biotic and abiotic stresses that are intensified by long production cycles. Production of seedless watermelon is also reliant on synchronized flowering of diploid pollenizers and the triploid watermelon cultivars. Utilizing marker-assisted selection (MAS) of flowering time in watermelon breeding would potentially aid in selection for early flowering, which would shorten the production time. A major quantitative trait locus Qdff3-1 (12–17 Mb) associated with days to female flower (R2 = 50%) was previously identified on chromosome 3 of watermelon. In this study, we validated the Qdff3-1 locus using QTL-seq. To determine more precisely the interval of Qdff3-1 and the candidate gene controlling flowering time, SNP markers were identified in the region and Kompetitive Allele Specific PCR (KASP) assays were developed for high-throughput genotyping. Markers were tested for trait association on the mapping population, recombinant F2:3 populations, and a panel of differential cultivars. In the KBS x NHM genetic background the QTL was delineated to a 1.13-Mb region, flanked by markers UGA3_14537958 and NW0248748. This region includes the FT and a protein phosphatase 2C (PP2C) gene. Genotyping the regions of interest in a panel of genetically diverse cultivars suggests that genetic control of flowering time in watermelon is dependent on the genetic background. These results lay the foundation for a greater understanding of flowering mechanisms in watermelon and improved breeding strategies for this trait. [ABSTRACT FROM AUTHOR]

Sharka, caused by plum pox virus, is the most important viral disease of stone fruits. Important progresses have been recently achieved in apricot ( Prunus armeniaca), identifying a major locus on chromosome 1 which explains most of the variability for plum pox virus (PPV) resistance trait. A set of molecular markers associated with the resistance has been developed and validated in different genetic backgrounds, endorsing their application for breeding purposes. Particularly for complex traits as the PPV resistance, requiring long and expensive phenotyping procedures, marker-assisted selection (MAS) bears a great potential to improve the efficiency of conventional breeding. In this work, novel HRM (high-resolution melting) assays were designed for the genotyping of resistant/susceptible alleles at PPV resistance (PPVres) locus. The assays were tested on 51 apricot cultivars and breeding selections already phenotyped for PPV resistance and cross-validated with standard short simple repeat marker data. We demonstrated that three HRM assays, PGS1.21_SNP, PGS1.24_SNP, and ZP002_DEL, represent a reliable, quick, and cost-effective genotyping approach, particularly suitable as high-throughput screening method for large-scale breeding programs. [ABSTRACT FROM AUTHOR]

The European hazelnut (Corylus avellana L.) is the most economically important nut species in the Betulaceae family. Despite the need for new improved hazelnut cultivars, few breeding programs are carried out because of the large plant size, the long lifecycle of the plant, and the expense and time required. To date, there are no reports of maps with quantitative trait loci (QTL) in hazelnut. Our objective in the present study was to identify QTL associated with vegetative traits to allow marker-assisted selection (MAS). An F1 progeny (275 plants) of Tonda Gentile delle Langhe × Merveille de Bollwiller obtained in 2009 was used to develop a QTL linkage map for vigour, sucker habit, and time of bud burst, after three years of observations. A set of 163 plants were analysed with 152 microsatellite markers. A map of 11 linkage groups was obtained, covering 663.1 cM, and 15 QTLs were identified and mapped for the traits examined. Of them, 10 were ‘major’ QTL, including a stably expressed region on LG_02 for leaf bud burst. At least one major QTL for each year underlies the variation in each trait and a clustering of QTL for trunk circumference and suckers/trunk circumference ratio with high inter-trait correlations was observed on LG_05, suggesting a single pleiotropic locus. This research represents an initial step in the future identification of chromosomal regions carrying genes of interest, important for breeding programs and MAS. [ABSTRACT FROM AUTHOR]

Molecular identification of wheat powdery mildew resistance (Pm) genes in breeding lines or cultivars is important for resistance breeding. Wanfengjian 34, a Chinese wheat breeding line with desirable agricultural performance in China, showed high level of resistance to powdery mildew at both seedling and adult stages. Genetic analysis demonstrated that the resistance to different Blumeria graminis f. sp. tritici isolates in Wanfengjian 34 was controlled by a single dominant Pm gene, temporarily designated PmWFJ. PmWFJ was mapped to chromosome arm 5DS and flanked by the simple sequence repeat marker Cfd81 and sequence characterized amplified region marker SCAR112 with genetic distance of 0.1 and 1.0 cM, respectively. PmWFJ shared the same locus with the documented Pm genes on the multi-allelic Pm2 locus by allelism tests between PmWFJ and Pm2 alleles, but showed unique powdery mildew reaction pattern compared with these documented Pm genes. Therefore, PmWFJ appears to be a new allele at the documented Pm2 locus. Four closely linked markers of PmWFJ were validated the applicability in 131 cultivar backgrounds for marker-assisted selection. [ABSTRACT FROM AUTHOR]

Wheat-Haynaldia villosa translocations T6V#2S.6AL and T6V#4S.6DL, carriers of Pm21 and PmV, respectively, continue to contribute powdery mildew resistance in wheat varieties in China. Based on colinearity between Brachypodium distachyon and Triticeae species, genomic sequences from gene intervals of B. distachyon physically linked to a homolog of Stpk-V, a key part of Pm21, were used to design primers and screen for codominant and stable markers. An anonymous marker, MBH1, tagging both Pm21 in 6V#2S and PmV in 6V#4S was identified. It also distinguished wheat 6AS- and 6DS-derived homoeoalleles of MBH1. Sequence length comparisons showed a decreasing order of 6AS > 6DS > 6V#2S > 6V#4S. F2 segregation analyses were conducted on crosses Yangmai 18 (T6V#2S.6AL)/Yangmai 19 and Yangmai 16/Yangmai 22 (T6V#4S.6DL). MBH1 detected homozygosity of both Pm21 and PmV in segregating populations. The results also showed that T6V#2S.6AL is more transmittable than T6V#4S.6DL. Using MBH1, we reconfirmed the identities of powdery mildew resistance genes in Yangmai 21, Zhenmai 9, and Yangmai 97G59. The resistance donor to all three was T6V#2S.6AL, indicating that the published pedigrees were not correct. Pm21 in NAU419-Y15, an intercalary translocation carrying Pm21, was also tagged by MBH1. MBH1 is a broadly applicable marker for selecting and distinguishing the translocation chromosomes carrying Pm21 and PmV, which continue to be effective in China. [ABSTRACT FROM AUTHOR]

It is important to detect wheat broad-spectrum powdery mildew resistance (Pm) genes in commercial cultivars with superior agronomic performance. YingBo 700, a Chinese commercial cultivar registered and released in 2012, showed a broad spectrum of resistance to 48 of 49 tested Blumeria graminis f. sp tritici (Bgt) isolates from different regions of China. Genetic analysis of F2 populations from the crosses YingBo 700 × Mingxian 169 and YingBo 700 × Shimai 15 and F2:3 lines from YingBo 700 × Mingxian 169 demonstrated that the resistance was controlled by a single dominant resistance gene, which was temporarily designated PmYB. Using molecular markers and bulked segregant analysis of the F2:3 lines from YingBo 700 × Mingxian 169, PmYB was mapped to the multi-allelic Pm2 region of chromosome arm 5DS co-segregated with the sequence-characterized amplified region (SCAR) marker SCAR112 and flanked by the simple sequence repeat (SSR) marker Cfd81 and SCAR marker SCAR203 with genetic distance of 0.9 and 1.9 cM, respectively. YingBo 700 showed a unique response pattern to different Bgt isolates compared with the lines with documented Pm2a, Pm2b, Pm48, PmLX66, PmW14, PmZ155 and PmX3986-2 on chromosome arm 5DS. Therefore, PmYB appears to be a novel allele in this multi-allelic region. In order to validate applicability of the closely linked markers for marker-assisted selection, the closely linked markers Cfd81, SCAR112, SCAR203 and Mag6176 were evaluated for applicability in diagnosing the resistance gene in 62 cultivars from different regions of China. The results will contribute to rapidly transfer of PmYB into more cultivars. [ABSTRACT FROM AUTHOR]

It is imperative to identify highly polymorphic and tightly linked markers of a known trait for molecular marker-assisted selection. Potyvirus resistance 4 ( Pvr4) locus in pepper confers resistance to three pathotypes of potato virus Y and to pepper mottle virus. We describe the use of next-generation sequencing technology to generate molecular markers tightly linked to Pvr4. Initially, comparative genomics was carried out, and a syntenic region of tomato on chromosome ten was used to generate PCR-based markers and map Pvr4. Subsequently, the genomic sequence of pepper was used, and more than 5000 single-nucleotide variants (SNVs) were identified within the interval. In addition, we identified nucleotide binding site-leucine-rich repeat-type disease resistance genes within the interval. Several of these SNVs were converted to molecular markers desirable for large-scale molecular breeding programmes. [ABSTRACT FROM AUTHOR]

Marker-assisted selection (MAS) for qualitative traits such as grain quality and resistance to certain diseases has proven to be highly effective. Multiple genes responsible for various quality components and disease resistances can be simultaneously stacked to boost the performance and to lengthen the commercial lifespan of high-yield varieties. Grain quality genes ( fgr and Wx) and three disease resistance genes ( Pita, Pik and Xa23) have been well characterized and used in MAS breeding. However, stacking all of them together into a single variety has not been reported. We reported here the stacking of the five genes into elite lines in rice. We achieved this through the development of functional markers from causal mutations at fgr, Wx and Pita, a gene-targeted marker at Pik and the use of a linked marker for Xa23. We employed and optimized the high-resolution melting (HRM) analysis method for use as the genotyping platform of fgr, Wx, Pik and Pita. By combining high-throughput DNA isolation, multiplex and nested-PCR methods, we showed that HRM could serve as cost-effective, highly automated, moderate-throughput and reliable non-gel genotyping platform for a small-scale MAS program. [ABSTRACT FROM AUTHOR]

Downy mildew is a fungal disease of sunflower that can lead to severe yield losses. The damage caused by the pathogen can be controlled by growing resistant sunflower varieties. Gene Pl was introgressed into cultivated sunflower from the wild species Helianthus argophyllus and provides resistance against all known downy mildew races. In this study, we used a mapping population from the cross-RHA 419/RHA-N-49. We identified a new co-segregating simple sequence repeat marker ORS675 and confirmed the co-segregation of markers ORS716 and ORS662 with Pl gene. The markers were validated on two registered resistant inbred lines RHA 443 and RHA 464, as well as on twenty inbred lines RH 1-20 obtained through methods of classical breeding. Molecular marker ORS716 was assessed for usefulness in selecting resistant progeny in 12 BC populations. Markers were found to be valuable for molecular breeding in diverse genetic backgrounds and enabled transfer of the resistance gene in different sunflower genotypes. [ABSTRACT FROM AUTHOR]

Potato virus Y (PVY, Potyvirus) is the fifth most important plant virus worldwide in terms of economic and scientific impact. It infects members of the family Solanaceae and causes losses in potato, tomato, tobacco, pepper and petunia production. In potato and its wild relatives, two types of resistance genes against PVY have been identified. While Ry genes confer symptomless extreme resistance, Ny genes cause a hypersensitive response visible as local necrosis that may also be able to prevent the virus from spreading under certain environmental conditions. The potato cultivar Sárpo Mira originates from Hungary and is highly resistant to PVY, although the source of this resistance remains unknown. We show that cv. Sárpo Mira reacts with a hypersensitive response leading to necrosis after PVY infection in detached leaf, whole plant and grafting assays. The hypersensitivity to PVY segregated amongst 140 individuals of tetraploid progeny of cvs. Sárpo Mira × Maris Piper in a 1:1 ratio, indicating that it was conferred by a single, dominant gene in simplex. Moreover, we identified five DNA markers linked to this trait and located the underlying locus ( Ny- Smira) to the long arm of potato chromosome IX. This position corresponds to the location of the Ry and Ny- 1 genes for PVY resistance. A simple PCR marker, located 1 cM from the Ny- Smira gene, can be recommended for selection of PVY-resistant progeny of cv. Sárpo Mira. [ABSTRACT FROM AUTHOR]

Globe artichoke ( Cynara cardunculus var. scolymus), whose immature inflorescences ( capitula) are consumed as a vegetable all over the world, contributes significantly to the agricultural economy of the Mediterranean basin. Here, we describe a QTL (quantitative trait loci) analysis aimed at elucidating the mode of inheritance of seven main and first-order capitulum traits. Mapping was carried out in an F population obtained by crossing a globe artichoke with a cultivated cardoon ( C. cardunculus var. altilis). A total of 100 QTL associated with the seven capitulum traits were mapped to 23 chromosomal regions, scattered over 12 of the 17 linkage groups. Among these, 73 were expressed in both growing seasons, while the others were only detected in one season. Up to nine QTL per trait were identified, and major QTL, responsible for some 20 % of the phenotypic variation, were detected for capitulum length, diameter, shape index and fresh weight. The QTL for correlated traits frequently co-localized, most likely due to pleiotropy. This study represents the first report on yield traits QTL in globe artichoke. The QTL identified, along with linked markers, particularly those located in four hot-spot QTL regions are of practical interest for crop improvement based on marker-assisted breeding. [ABSTRACT FROM AUTHOR]

Quantitative trait locus (QTL) analyses have greatly enhanced our understanding of complex traits in rice ( Oryza sativa). In parallel, the development of introgression lines has provided a powerful tool for elucidation of complicated genetic networks and identification of QTL. We recently developed a biotron breeding system that allows rapid indoor cultivation of rice plants. The system, however, has two relatively weak points in its application to marker-assisted breeding in rice: first, variation in generation times among cultivars; second, the low number of seeds produced by crosses. To compensate for these weaknesses, we propose utilizing cytoplasmic male sterility (CMS) and restorer (Rf) lines with a cv. Nipponbare genetic background. Through use of the Nipponbare genetic background, rice generation times of 2 months can be achieved regardless of any differences in the genetic background of the donor rice plant. This CMS–Rf system confers a high yield of hybrid seeds, avoids the need for emasculation and precludes accidental crosses. Our results demonstrate that this new methodology can markedly accelerate many different aspects of rice research, especially in functional genomics. The combination of biotron breeding system, early flowering habit and CMS will be of great value for screening candidate genes associated with QTL and for introducing useful QTL into elite cultivars. [ABSTRACT FROM AUTHOR]

The primary aim of plant breeders is to develop new cultivars in order to improve productivity and to combat threats from pests and diseases. Recent advances in genomics have been recognised as providing important tools for plant breeders in the form of molecular genetic markers that can be used to tag genes of interest. However, the cost-effective use of marker technology is dependent on the nature and timing of the use of such markers. A conventional potato breeding programme typically creates a large breeding population and then employs phenotypic recurrent selection over a number of generations to identify superior genotypes. Marker-assisted selection (MAS) provides the advantage of being applicable at the seedling or an early generation stage. We have analysed the cost of MAS and compared it to conventional screening, then modelled the respective costs against the breeding population size of the generation in which they would be applied to determine whether MAS in the early generations of a potato breeding programme would be cost-effective. As various potato breeding programmes employ different selection rates in early generations, these rates have also been modelled to determine the effect. Our results indicate that MAS could be applied cost-effectively in the second clonal generation for all models currently employed in potato breeding. [ABSTRACT FROM AUTHOR]

The waxy ( wx) gene in maize is associated with higher content of amylopectin in the endosperm and better flavor. The opaque- 16 ( o16) gene is associated with higher lysine content in the endosperm and better nutritional value. To pyramid the wx and o16 genes, cross and backcross populations were constructed using the o16 line QCL3024 and the two waxy lines, QCL5019 and QCL5008, as parents. The linkage marker umc1141 for the o16 gene and the internal marker phi027 for the wx gene were used to select the target genes. Simple sequence repeat markers covering the whole genome were used for background selection in individual progenies of the backcross population. The grain lysine content was determined using the Acid Orange-12 Dye Binding Lysine method. Qualitative and quantitative analyses of the grain content of amylopectin were performed using the I-KI procedure and double-wavelength spectrophotometry, respectively. Four lines of the double recessive genotype wxwxo16o16 were obtained from the F4 generation of the cross population and three lines of the same genotype were obtained from the BC2F4 generation of the backcross population. The lysine content of the pyramid lines was 16-27 and 18-28 % higher than the waxy parents QCL5019 and QCL5008, respectively. The pyramid lines had 61-63 % more amylopectin than the high-lysine parent QCL3024. The three pyramid lines from the backcross population had similar genetic background to the waxy parent QCL5008. Our results are of significance for the improvement of maize quality. [ABSTRACT FROM AUTHOR]

Rice blast is one of the most serious diseases in rice ( Oryza sativa L.) worldwide. Jin 23B is the maintainer line, a parent for a number of hybrid rice varieties used widely in China. However, Jin 23B is highly susceptible to rice blast. In this study, Pi1, Pi2, and D12 were introgressed to improve the blast resistance of Jin 23B and its derived hybrids, Jinyou 402 and Jinyou 207, by marker-assisted selection (MAS). The improved Jin 23B, which carried single, two, and three genes, were evaluated for their resistance to rice blast using natural inoculation methods in disease nursery of Xianfeng, Hubei, China. The results showed that, the greater the number of genes contained in the improved Jin 23B and hybrids, the higher the resistance to rice blast. Pi1, Pi2, and D12 showed a strong dosage effect on the resistance to blast in the hybrid background during the entire growth duration in the field condition, being very useful for breeding blast-resistant hybrids. The result of examining agronomic traits showed that the improved Jin 23B and its derived hybrid rice were taller than or similar to controls, when there was no disease stress. [ABSTRACT FROM AUTHOR]

The brown planthopper (BPH) is the most devastating insect pest in rice-producing areas. Shanyou 63 has become a widely cultivated hybrid in China over the last two decades; however, this line has become increasingly susceptible to bacterial blight (BB), blast, and BPH, resulting in a rapid decline in its use in rice production. In this study, a molecular marker-assisted selection (MAS) introgression of Bph14 and Bph15 was performed to improve the BPH resistance of Minghui 63 and its derived hybrids such as Shanyou 63. The effect of pyramiding genes was then comprehensively evaluated using three tests that comprised seedbox screening, feeding rate, and antixenosis for settling in the field. The results showed that the improved hybrids containing a single BPH resistance gene showed enhanced resistance (lower resistance score, honeydew weight and number of BPH settling) compared to conventional hybrids, while pyramiding two genes provided even higher resistance. Moreover, both Bph14 and Bph15 are partial dominance genes, and have a strong dosage effect on the resistance to BPH in the hybrid background, which is useful for breeding BPH-resistant hybrids. Field trial data demonstrated that yields of improved hybrid rice were higher than or similar to the control (Shanyou 63) under natural field conditions. These improved versions could be used in breeding programs for 'green super rice.' [ABSTRACT FROM AUTHOR]

Bipolaris sorokiniana (teleomorph: Cochliobolus sativus) is the fungal pathogen responsible for spot blotch in barley ( Hordeum vulgare L.) and occurs worldwide in warmer, humid growing conditions. Current Australian barley varieties are largely susceptible to this disease and attempts are being made to introduce sources of resistance from North America. In this study we have compared chromosomal locations of spot blotch resistance reactions in four North American two-rowed barley lines; the North Dakota lines ND11231-12 and ND11231-11 and the Canadian lines TR251 and WPG8412-9-2-1. Diversity arrays technology-based PCR, expressed sequence tag and SSR markers have been mapped across four populations derived from crosses between susceptible parental lines and these four resistant parents to determine the location of resistance loci. Quantitative trait loci (QTL) conferring resistance to spot blotch in adult plants (APR) were detected on chromosomes 3HS and 7HS. In contrast, seedling resistance (SLR) was controlled solely by a locus on chromosome 7HS. The phenotypic variance explained by the APR QTL on 3HS was between 16 and 25% and the phenotypic variance explained by the 7HS APR QTL was between 8 and 42% across the four populations. The SLR QTL on 7HS explained between 52 and 64% of the phenotypic variance. An examination of the pedigrees of these resistance sources supports the common identity of resistance in these lines and indicates that only a limited number of major resistance loci are available in current two-rowed germplasm. [ABSTRACT FROM AUTHOR]

Molecular breeding for pathogen resistance faces two major problems that delay its widespread adoption, resistance breakdown and difficulties in unambiguously identifying the alleles of the markers associated with specific resistance genes. Since the breakdown of the Rvi6 ( Vf) gene in the Northern part of Europe breeders have intensified the search for new resistance sources to be introduced into their breeding programs. Alternative major genes to Rvi6 are available (e.g. Rvi2, Rvi4, Rvi5, Rvi10; Rvi11, Rvi12, Rvi13, and Rvi15, respectively Vh2, Vh4, Vm, Va, Vbj, Vb, Vd, Vr2 according to the old apple scab resistance gene nomenclature) but, with few exceptions (i.e., Rvi4, Rvi5 and, Rvi13), they have so far not been incorporated in commercial varieties. Pyramiding, i.e., combining several of these major resistance genes (R-genes) in individual plants, is one of the most promising strategies currently available to develop apple cultivars with durable apple scab resistance. But, which genes are the best suited to produce such new cultivars? Although the most interesting genes are surely those whose resistance so far has not been broken by the pathogen, genes with resistance that has been overcome coupled with only limited spread of the virulence may also be used in the pyramiding process. However, obtaining information on whether an R-gene is overcome and if so, the extent of the spread of the virulence is difficult and time consuming. Furthermore, often such reports are not up-to-date and the correctness of the data is difficult to verify. To solve these problems, the initiative “Monitoring of Venturia inaequalis virulences” has been proposed. The monitoring is based on a network of orchards of selected differential hosts. Incidence and severity of scab on these genotypes will be collected yearly; and after validation, the data will be published through the homepage of the project (). Here, we present an outline of this initiative. A second major obstacle for broad adoption of marker assisted selection is the lack of tools to align marker analyzes performed in different laboratories to unambiguously identify the alleles linked to specific resistances. The identification of the alleles of the markers in coupling with the resistance genes is often very difficult, if the same genotype used to develop the markers is not simultaneously analyzed. In this paper we present an approach to standardize the size of the alleles in coupling with the resistance genes, using easily accessible cultivars. The proposed procedure has been applied to selected markers for the apple scab resistance genes Rvi2, Rvi4, Rvi5, Rvi6, Rvi11, Rvi12, Rvi13, Rvi14 and Rvi15 (respectively Vh2, Vh4, Vm, Vf, Vbj, Vb, Vd, Rvi14 and Vr2 according to the old nomenclature). [ABSTRACT FROM AUTHOR]

Inheritance of covered smut resistance was investigated in three hulless × hulled barley populations (CDC Candle/Q21861, CDC McGwire/Q21861, and CDC McGwire/TR640). Greenhouse and/or field screening indicated resistance was controlled by a single major gene from Q21861 and TR640. Three molecular markers (UhR 450, aHor 2 and OPO6780) linked to the covered smut resistance gene ( Ruhq) in the hulled line Q21861 were assessed for their usefulness in selecting resistant hulless barley. All markers were linked to covered smut resistance in the three populations evaluated, although aHor 2 was only polymorphic in CDC Candle/Q21861. Two strategies, doubled haploidy (DH) and marker-assisted backcrossing (MAB), were used to simultaneously introgress Ruhq and loose smut resistance ( Run8) into the hulless barley cultivar CDC McGwire. Thirty-five DH lines were developed from a cross of hulless loose smut resistant line SH00752 (CDC McGwire/TR251) by hulless covered smut resistant line SH01470 (CDC McGwire/Q21861). By screening the 35 DH lines for each of the markers, 14 were identified as positive for both. Following three rounds of screening by artificial inoculation, 12 of those were identified as resistant to both diseases. In the MAB program, “blind” selection based solely on markers was conducted through the BC3F2 generation; lines resistant to both diseases were obtained. One line, designated HB390, is being advanced to 2nd year of the Western Canadian Hulless Barley Co-operative yield trials, the final step to release of a cultivar for commercial production in Canada. These results confirm that molecular markers can be used in either DH or MAB programs to assist in the rapid introgression of simply inherited disease resistance genes into elite lines, with considerable time and cost savings. [ABSTRACT FROM AUTHOR]

Cannabis sativa is an interesting crop for several industrial uses, but the legislations in Europe and USA require a tight control of cannabinoid type and content for cultivation and subsidies release. Therefore, cannabinoid survey by gas chromatography of materials under selection is an important step in hemp breeding. In this paper, a number of Cannabis accessions were examined for their cannabinoid composition. Their absolute and relative content was examined, and results are discussed in the light of both the current genetic model for cannabinoid’s inheritance, and the legislation’s requirements. In addition, the effectiveness of two different types of markers associated to the locus determining the chemotype in Cannabis was evaluated and discussed, as possible tools in marker-assisted selection in hemp, but also for possible applications in the forensic and pharmaceutical fields. [ABSTRACT FROM AUTHOR]

Quantitative trait locus (QTL) analyses are used by geneticists to characterize the genetic architecture of quantitative traits, provide a foundation for marker-aided-selection (MAS), and provide a framework for positional selection of candidate genes. The most useful QTL for breeding applications are those that have been verified in time, space, and/or genetic background. In this study, spring cold-hardiness of Douglas-fir foliar tissues was evaluated in two clonally replicated (n=170 and 383 clones) full-sib cohorts derived from the same parental cross in two different years (made 5 years apart). The cohorts were established in widely separated forest test sites and tissues were artificially freeze tested using different cold injury assessment methods. Four of six unique QTL detected for spring cold-hardiness in needles of Cohort 1 were tentatively verified in the second cohort. Four additional QTL were detected in Cohort 2, two on linkage groups (LGs) not previously represented in the smaller cohort. In total, 10 unique QTL were identified across both cohorts. Seventeen of twenty-nine putative cold-hardiness candidate genes (Douglas-fir ESTs) placed on the Douglas-fir linkage map locate within the 95% confidence intervals of spring needle cold-hardiness QTL from the two cohorts and thus represent priority targets for initiating association mapping in Douglas-fir. [ABSTRACT FROM AUTHOR]

Primers were developed for 118 microsatellites isolated from grape (Vitis vinifera) genomic libraries enriched for (AC)n repeats. Only one microsatellite sequence matched other grape SSR-sequences in the GeneBank database. Genotyping was carried out in the parental lines and four offspring of two pseudo-test-cross populations, ‘Cabernet Sauvignon’ x ‘Seyval’ and ‘Chardonnay’ x ‘Bianca’, and a further six other grape genotypes (V. vinifera ‘Sultanina’, ‘Merlot’, ‘Syrah’, ‘Müller-Thurgau’, Vitis ‘Regent’ and V. riparia ‘Gloire de Montpellier’). A total of 108 microsatellites showed easily scorable alleles and 100 of them segregated according to a configuration suitable for mapping in either cross. A further 8 SSRs, although unsuitable for mapping in those crosses, showed polymorphism in the other genotypes tested. This set of markers was used, along with 75 microsatellites of other repeat-types, to fingerprint 46 offspring of the cross ‘Chardonnay’ x ‘Bianca’. For each full-sib, individual heterozygosity and distance in repeat units between pairs of alleles at each locus (meand2) were calculated as a tool for predicting ‘highly outbred’ recombinant individuals. Six microsatellites with segregation ratios significantly distorted towards the lack of homozygous sibs were identified and mapped to linkage groups LG 3 and LG 5. Estimation of heterozygosity at genome-wide level and genotyping at loci for which homozygous sibs are discriminated against are discussed for marker-assisted background selection in outcrossing grapevines. [ABSTRACT FROM AUTHOR]

A novel locus for extreme resistance toPotato virus Y(PVY),Ry-f sto, was identified on potato chromosome XII. The geneRy-f sto has been introgressed from the wild potato speciesSolanum stoloniferum. Inheritance ofRy-f sto in the tetraploid potato population Rysto was consistent with the model of a single, dominant gene. Bulked segregant analysis identified an ISSR (inter-simple sequence repeat) marker UBC 857980 linked toRy-f sto. This marker mapped to linkage group XII of a reference potato RFLP (restriction fragment length polymorphism) map. Chromosome XII specific RFLP markers were converted into PCR-based STS and CAPS markers and tested for linkage withRy-f sto in the population Rysto. CAPS marker GP122718 was tightly linked to the resistance gene and was successfully used to identify Polish and German cultivars expressing extreme resistance to PVY. This indicates that the source ofRy-f sto has been widely utilized in various potato breeding programs and can be monitored by a diagnostic marker in marker-assisted selection. [ABSTRACT FROM AUTHOR]

Blackmold, caused by the fungus Alternaria alternata, is a major ripe fruit disease of processing tomatoes. Previously, we found blackmold resistance in a wild tomato ( Lycopersicon cheesmanii) and quantitative trait loci (QTL) for resistance were mapped in an interspecific population. Five QTLs were selected for introgression from L. cheesmanii into cultivated tomato using marker-assisted selection (MAS). Restriction fragment length polymorphism and PCR-based markers flanking, and within, the chromosomal regions containing QTLs were used for MAS during backcross and selfing generations. BC1 plants heterozygous at the QTLs, and subsequent BC1S1 and BC1S2 lines possessing different homozygous combinations of alleles at the target QTLs, were identified using DNA markers. Field experiments were conducted in 1998 (with 80 marker-selected BC1S2 lines) and 1999 (with 151 marker-selected BC1S2 and BC1S3 lines) at three California locations. Blackmold resistance was assessed during both years, and horticultural traits were evaluated in 1999. The BC1S2 and BC1S3 lines containing L. cheesmanii alleles at the QTLs were associated with a large genetic variance for resistance to blackmold and moderate heritability, suggesting that significant genetic gain may be achieved by selection in this genetic material. L. cheesmanii alleles at three of the five introgressed QTLs showed a significant, positive effect on blackmold resistance. A QTL on chromosome 2 had the largest positive effect on blackmold resistance, alone and in combination with other QTLs, and was also associated with earliness, a positive horticultural trait. The other four QTLs were associated primarily with negative horticultural traits. Fine mapping QTLs using near isogenic lines could help determine if such trait associations are due to linkage drag or pleiotropy. [ABSTRACT FROM AUTHOR]

Microsatellite markers have many of the properties of an ideal marker, but development of microsatellite markers is tedious, time-consuming and expensive. In the past few years, great efforts have been made to develop, map and utilize microsatellite markers in various crops. It is still a major challenge to find a microsatellite marker associated with an economically important trait. In the present study we report on the targeted development of a microsatellite marker to a barley disease resistance gene. The method includes the following steps: (1) pooling DNA samples from a segregating population based on the principle of bulked-segregant analysis; (2) digesting the pooled DNAs and ligating adaptors; (3) selectively amplifying and identifying polymorphic microsatellites; and (4) developing primers for the microsatellite associated with the targeted trait. Using this method, a microsatellite marker associated with the true loose smut resistance gene ( Un8) in the Harrington × TR306 doubled-haploid population was identified. This marker showed polymorphism in four breeding populations segregating for true loose smut resistance. In three of these populations, genetic distance between the microsatellite and the true loose smut resistance gene varied from 8.6 to 10.3 cM. Polymorphism of the microsatellite was tested among three disease resistant lines and 21 susceptible cultivars. Fourteen to eighteen of the 21 susceptible cultivars exhibited a polymorphism for the microsatellite with respect to at least one of the disease-resistant lines. This method for the targeted development of microsatellite markers should have widespread applicability and should efficiently provide highly polymorphic markers for use in breeding programs. [ABSTRACT FROM AUTHOR]

RAPD markers generated by mixtures of two different primers were developed for octoploid × Tritordeum (amphiploid Hordeum chilense × Triticum aestivum) and its parents. Addition lines were used to identify 21 specific RAPD markers for the H. chilense chromosomes detectable in a wheat background. Ten RAPD bands were selected and eight of them were converted into dominant SCAR markers by direct sequencing of the RAPD products, avoiding the costly and time-consuming cloning step. The methodology overcomes some of the pitfalls associated with the election of the right clones when developing SCARs from RAPD markers. The SCARs generated have maintained both the chromosome specificity and the possibility of detection in a wheat background. This strategy provides a rapid method for the characterization of RAPD markers and for the development of PCR-based markers for both the characterization of the introgression of H. chilense in bread and durum wheat, as well as the efficient and reliable screening of tritordeum lines. [ABSTRACT FROM AUTHOR]

A simple and robust multiplex PCR approach was developed for detection of the alleles Ry-fsto and Ns conferring resistance of potato to Potato Virus Y (PVY) and Potato Virus S (PVS), respectively. Cleaved amplified polymorphic sequence (CAPS) markers GP122564 linked to Ry-fsto and SC811260 linked to Ns were amplified in one PCR reaction and identified after simultaneous digestion of the amplicons with restriction enzymes EcoRV and MboI. Effectiveness of this procedure for marker-assisted selection was confirmed in 55 potato cultivars. [ABSTRACT FROM AUTHOR]

Cadmium (Cd) is a toxic element that can accumulate in rice grains, presenting a threat to human health. Indica rice hybrid is dominant in southern China, and this genetic background is linked to high-level Cd accumulation in grains. Thus, lowering grain Cd levels in indica hybrids is a priority in the breeding programs. Previously, a locus on chromosome 7 was found to be associated with grain Cd variation in 617 rice hybrids and exhibited apparent indica–japonica differentiation. In this present study, a backcross population was generated to investigate the genetic control of this locus, as qCd7, on grain Cd performance in rice. Quantitative trait locus (QTL) analysis revealed qCd7 as an incomplete dominant factor that has a major effect on grain Cd variation; the 'NPB' allele can reduce grain Cd content. Using a 3 × 13 NCII design population, we evaluated qCd7's potential to decrease grain Cd content in indica hybrid combinations, and phenotypic comparisons indicated that introgression of qCd7-NPB effectively reduced grain Cd accumulation. Combining ability analysis revealed that parental lines carrying qCd7-NPB consistently displayed negative general combination ability (GCA) effects on grain Cd accumulation, which could be used to predict stable combiners in breeding programs. These results suggest that introgression of qCd7-NPB has great potential to decrease grain Cd content in indica hybrid breeding, which suggested that identifying allelic variation derived from indica–japonica genetic differences could facilitate genetic improvement in low grain Cd indica hybrid breeding programs. [ABSTRACT FROM AUTHOR]

FAE1, the gene encoding fatty acid elongase, has been implicated to play a decisive role in the synthesis of erucic acid. Allelic variations in this gene, such as single nucleotide polymorphisms (SNPs), insertions/deletions (InDels), and insertions of transposable element (TE), are predominantly responsible for variability in erucic acid content in the seed, among the Brassica genotypes. Brassica juncea being an amphidiploid, contains two paralogs, FAE1.1 and FAE1.2. Although the coding DNA sequences (CDS) of FAE gene is highly conserved (> 95% identical), the promoter region is found to be polymorphic. The sequence variability in the promoter region of FAE1 across different Brassica spp. suggests their likely involvement in the regulation of the gene expression. This study was aimed to evaluate polymorphism in the upstream region of FAE1.1 and FAE1.2 genes, across the low erucic acid (LEA) and high erucic acid (HEA) cultivars, and to develop molecular markers based on this variability. The upstream regions of FAE were sequenced from LEA cultivar "Pusa Mustard 30" and HEA cultivar "Pusa Bold." A 28-bp deletion in the promoter of FAE1.1 and a 340-bp insertion of a transposon-like element in the FAE1.2 gene promoter were discovered in LEA genotype. Markers based on the sequence variability in the promoter regions of FAE1.1 and FAE1.2 were found to completely co-segregate with the seed erucic acid content. These markers can be effectively used in marker-assisted selection for development of low erucic acid cultivars in B. juncea. [ABSTRACT FROM AUTHOR]

Durum wheat (Triticum durum Desf.) is a major crop of North Africa. Here, its production is affected by Hessian fly (Mayetiola destructor, HF) epidemics. Genetic resistance against this pest exist, but its molecular basis remains unclear. Here, a panel of 159 modern durum lines were exposed to the Moroccan HF biotype. Association mapping studies revealed three major loci conferring resistance. QH.icd-2A was identified at LOD of 24.1 on the telomeric end of 2AL, and it is believed to represent a novel locus derived from T. dicoccum. QH.icd-5B was identified on 5BS at LOD of 9.5, and it appears as overlapping with H31. QHara.icd-6B was identified at LOD of 54.5. This locus confers resistance to five Moroccan released cultivars, including 'Faraj'. A mapping population (MP) was obtained by crossing 'Faraj' and a HF-susceptible cultivar 'Gidara2'. Challenging this MP with the Moroccan and Great Plains HF biotypes revealed 1:1 segregation ratio fitting of a single gene. Quantitative trait locus (QTL) analysis confirmed a single locus at LOD of 35 and 25 for the two biotypes, respectively, corresponding to QHara.icd-6B. This locus spans a 7.7 cM interval, and it is derived via introgression from a resistant T. araraticum. One KASP marker (BS00072387) was validated for use in breeding on a separate set of elite lines, to show r2 of 0.65 and accuracy of 0.98. Finally, field testing across sites did not identify any yield drag for QHara.icd-6B. The work presented here provides ideal tools to incorporate HF-resistant loci in durum cultivars via marker-assisted breeding. [ABSTRACT FROM AUTHOR]

Fusarium wilt, Fusarium oxysporum f. sp. niveum (FON), of watermelon (Citrullus lanatus) is a fungal pathogen that causes significant yield losses in the US watermelon industry. FON damages watermelon through invasion of the root system and remains a difficult pathogen to manage due to its long-lasting survival spores which persist in the soil. Chemical control options for this pathogen are lacking, making development of genetic resistance the best option. There are four known races of FON (0, 1, 2, and 3) which are distinguished based on their pathogenicity of differential cultivars. Most modern cultivar releases have FON race 1 (FON-1) resistance, which has been mapped on the end of chromosome 1. Application of marker assisted selection (MAS) would improve the efficiency of FON-1 resistance breeding. In order to identify markers for selection in the FON-1 region, the QTL-seq method was utilized on an F2 population segregating for FON-1 resistance. Single nucleotide polymorphism (SNP) markers in the region were developed into Kompetitive allele-specific PCR (KASP™) assays and tested for trait association on the segregating F2:3 population. Marker validation was done using an F2 population from a cross between FON-1 susceptible "New Hampshire Midget" and FON-1-resistant "Calhoun Gray." Further validation on a panel of susceptible and resistant cultivars and Plant Introductions identified SNP marker UGA1_502161 as a useful marker for selection of FON-1 resistance from Calhoun Gray. [ABSTRACT FROM AUTHOR]