Improvement of Cercospora leaf spot and powdery mildew resistance of mungbean variety KING through marker-assisted selection

The development of resistant mungbean varieties is one of the most efficient strategies to control major diseases such as Cercospora leaf spot (CLS) and powdery mildew (PM). The objectives of this study were to pyramid a CLS resistance gene and two PM resistance genes from the donor parent D2 into a susceptible variety KING through marker-assisted backcrossing (MABC) and to evaluate their agronomic traits and disease resistance under field conditions. Five markers linked to the resistance genes were used for foreground selection, while two marker sets [Set A containing 15 polymorphic simple sequence repeat (SSR) and expressed sequence tag-SSR (EST-SSR) markers and Set B containing 34 polymorphic inter-simple sequence repeat (ISSR) loci] were also used for background selection. Two pyramided backcross (BC) lines, namely H3 and H4, were homozygous at all five marker loci when confirmed in BC4F4 and BC4F5 generations. Their recurrent parent genome (RPG) recovery ranged from 96.4 to 100.0%, depending on the marker sets. During field evaluation, a moderate to high level of CLS and PM resistance was observed in both BC lines compared to the susceptible recurrent parent KING. One of these BC lines (H3) had all agronomic traits similar or superior to the recurrent parent KING at all environments, and had a higher yield than KING (18.0–32.0%) under CLS and PM outbreaks. This line can be developed into a new resistant mungbean variety in Thailand in the future. These results substantiate the usefulness of MABC for transferring multiple resistance genes into an elite variety.

Genome survey sequencing and characterization of simple sequence repeat (SSR) markers in Platostoma palustre (Blume) A.J.Paton (Chinese mesona)

Platostoma palustre (Blume) A.J.Paton is an annual herbaceous persistent plant of the Labiatae family. However, there is a lack of genomic data for this plant, which severely restricts its genetic improvement. In this study, we performed genome survey sequencing of P. palustre and developed simple sequence repeat (SSR) markers based on the resulting sequence. K-mer analysis revealed that the assembled genome size was approximately 1.21 Gb. A total of 15,498 SSR motifs were identified and characterized in this study; among them, dinucleotide, and hexanucleotide repeats had the highest and lowest, respectively. Among the dinucleotide repeat motifs, AT/TA repeat motifs were the most abundant, and GC/CG repeat motifs were rather rare, accounting for 44.28% and 0.63%, respectively. Genetic similarity coefficient analysis by the UPMGA methods clustered 12 clones, of P. palustre and related species into two subgroups. These results provide helpful information for further research on P. palustre resources and variety improvements.

Analysis of genetic diversity in selected sugarcane (Saccharum officinarum L.) accessions using inter simple sequence repeat (ISSR) markers

<p class="042abstractstekst"><span lang="EN-US">Genetic diversity information among a population is important in exploiting heterozygosity for the improvement of crop species through breeding programmes. This study was therefore, conducted to assess genetic diversity and establish molecular relationships among 20 selected exotic sugarcane accessions from the Unilorin Sugar Research Institute germplasm using Inter Simple Sequence Repeat (ISSR) molecular markers. Genomic DNA was extracted from the sugarcane leaf. Fragments amplification was then performed by polymerase chain reaction (PCR) with ISSR markers and the data obtained were analyzed using MEGA 4 software. Analysis of the electropherogram showed a total of 39 loci consisting of 369 bands, out of which 95.8% were polymorphic. The biplot analysis showed all the markers contributed to the observed diversity with the least achieved with ISSR6. The principal co-ordinate analysis grouped the accessions into four clusters, comprising mixtures of all the six collection sites. The polymorphism obtained in the present study showed that the ISSR markers are effective for assessment of genetic diversity of the sugarcane accessions as it reveals the genetic similarity or divergence of the accessions regardless their place of origin or cultivation.</span></p>

Development of SSR Databases Available for Both NGS and Capillary Electrophoresis in Apple, Pear and Tea

Developing new varieties in fruit and tea breeding programs is very costly and labor-intensive. Thus, establishing a variety discrimination system is important for protecting breeders’ rights and producers’ profits. Simple sequence repeat (SSR) databases that can be utilized for both next-generation sequencing (SSR-GBS) and polymerase chain reaction–capillary electrophoresis (PCR-CE) would be very useful in variety discrimination. In the present study, SSRs with tri-, tetra- and pentanucleotide repeats were examined in apple, pear and tea. Out of 37 SSRs that showed clear results in PCR-CE, 27 were suitable for SSR-GBS. Among the remaining markers, there was allele dropout for some markers that caused differences between the results of PCR-CE and SSR-GBS. For the selected 27 markers, the alleles detected by SSR-GBS were comparable to those detected by PCR-CE. Furthermore, we developed a computational pipeline for automated genotyping using SSR-GBS by setting a value “α” for each marker, a criterion whether a genotype is homozygous or heterozygous based on allele frequency. The set of 27 markers contains 10, 8 and 9 SSRs for apple, pear and tea, respectively, that are useful for both PCR-CE and SSR-GBS and suitable for automation. The databases help researchers discriminate varieties in various ways depending on sample size, markers and methods.

Evaluation and Pre-selection of New Grapevine Genotypes Resistant to Downy and Powdery Mildew, Obtained by Cross-Breeding Programs in Spain

The need to develop an environmentally friendly, sustainable viticulture model has led to numerous grapevine improvement programmes aiming to increase resistance to downy and powdery mildew. The success of such programmes relies on the availability of protocols that can quantify the resistance/susceptibility of new genotypes, and on the existence of molecular markers of resistance loci that can aid in the selection process. The present work assesses the degree of phenotypic resistance/susceptibility to downy and powdery mildew of 28 new genotypes obtained from crosses between “Monastrell” and “Regent.” Three genotypes showed strong combined resistance, making them good candidates for future crosses with other sources of resistance to these diseases (pyramiding). In general, laboratory and glasshouse assessments of resistance at the phenotype level agreed with the resistance expected from the presence of resistance-associated alleles of simple sequence repeat (SSR) markers for the loci Rpv3 and Ren3 (inherited from “Regent”), confirming their usefulness as indicators of likely resistance to downy and powdery mildew, respectively, particularly so for downy mildew.

Spatial and temporal genetic variation in Ethiopian barley (Hordeum vulgare L.) landraces as revealed by simple sequence repeat (SSR) markers

Background Ethiopia is considered as center of diversity for barley (Hordeum vulgare L.) and it is grown across different agro-ecologies of the country. Unraveling population structure and gene flow status on temporal scales assists an evaluation of the consequences of physical, demographic and overall environmental changes on the stability and persistence of populations. This study was to examine spatial and temporal genetic variation within and among barley landrace samples collected over a period of four decades, using simple sequence repeat markers. Results Results from STRUCTURE, neighbor joining tree and discriminant analysis of principal component (DAPC) analysis revealed presence low-to-high genetic diversity among the landraces and grouped the landraces into three clusters. The cluster analysis revealed a close relationship between landraces along geographic proximity with genetic distance increases along with geographic distance. From analysis of molecular variance (AMOVA) in terms of collection year, it was observed that within-population genetic diversity much higher than between population and that the temporal differentiation is considerably smaller. The low-to-high genetic differentiation between landraces could be attributed to gene flow across the region as a consequence of seed exchange among farmers. Conclusion The results demonstrate that this set of SSRs was highly informative and useful in generating a meaningful classification of barley germplasms. Furthermore, results obtained from this study also suggest that landraces are a source of valuable germplasm for sustainable agriculture in the context of future climate change and in situ conservation strategies following adaptation to local environments.