Phenotypic and DNA Marker-Assisted Characterization of Russian Potato Cultivars for Resistance to Potato Cyst Nematodes

Potato is one of the most important food crops in the world and also in the Russian Federation. Among harmful organisms reducing potato yield potential, the potato cyst nematodes (PCN) are considered to be ones of the most damaging pests. Information on PCN resistant cultivars is important for potato breeding and production. Russian potato cultivars are characterized in the state-bio-test program for resistance to only one PCN species Globodera rostochiensis and one pathotype Ro1 which is reported to be present in the country. This study aimed to find domestic cultivars with multiple resistances to different PCN species and different pathotypes using phenotyping coupled with molecular marker analysis due to the risk of the occasional introduction of new pests. The phenotypic response was determined by the inoculation of plants with pathotypes Ro5 of G. rostochiensis and Pa3 of G. pallida. The obtained results were supplemented by the state-bio-test data on resistance to Ro1 of G. rostochiensis. Nine of 26 Russian cultivars were resistant both to Ro5 and Ro1 pathotypes and two cultivars possess multiple resistances to both PCN species. Most tested molecular markers associated with the Gpa2, GpaVvrn, GpaVsspl, Grp1 loci showed discrepancies with phenotyping. However, a predictive haplotype and epistatic effect were detected.

Developing Novel Rice Genotypes Harboring Specific QTL Alleles Associated with High Grain Yield under Water Shortage Stress

Rice is considered a strategic crop for many countries around the world, being the main cash crop for farmers. Water shortage stress occurrence as a result of climate change is among the main threats challenging rice breeders in the last few decades. In the current study, 19 Fn-lines were developed from four populations by crossing a reverse thermo-responsive genic male sterile (rTGMS) line, M.J.5460S, with the three high-quality Egyptian commercial cultivars Giza177, Sakha105, Sakha106 and the promising line GZ7768 as male parents. These newly developed lines, along with their parents, and two water shortage stress-tolerant international genotypes (Azucena and IRAT170), were cultivated under water-shortage stress conditions and compared with their performance under well-watered conditions. Results indicated that the yielding ability of the 19 newly developed lines exceeded those for the two Egyptian parents (Giza177 and Sakha105) under well-watered conditions. The lines M.J5460S/GIZA177-3 and M.J5460S/GIZA177-12 were the best performing genotypes under water shortage stress conditions. The genetic and heritability in broad sense estimates indicated that direct selection for grain yield (GY) under water-shortage stress is highly effective in the current study. Molecular marker analysis revealed that M.J5460S/GIZA177-3 had accumulated the quantitative trait loci (QTL)s, on the chromosomes 2, 3, and 9, which contribute to GY under water-shortage stress from their high yielding tolerant ancestor, M.J5460S. It could be concluded that those lines are high yielding under both well-watered and water-stress conditions harboring several QTLs for yield enhancement under both conditions and that the markers RM555, RM14551, RM3199, RM257, RM242, and RM410 are among the markers that could be used in marker-assisted selection (MAS) breeding programs for such stress condition.

Characterization of chromosome constitution in three wheat - Thinopyrum intermedium amphiploids revealed frequent rearrangement of alien and wheat chromosomes

Background Thinopyrum intermedium (2n = 6x = 42) is an important wild perennial Triticeae species exhibiting many potentially favorable traits for wheat improvement. Wheat-Th. intermedium partial amphiploids serve as a bridge to transfer desirable genes from Th. intermedium into common wheat. Results Three octoploid Trititrigia accessions (TE261–1, TE266–1, and TE346–1) with good resistances to stripe rust, powdery mildew and aphids were selected from hybrid progenies between Th. intermedium and the common wheat variety ‘Yannong 15’ (YN15). Genomic in situ hybridization (GISH), fluorescence in situ hybridization (FISH) and multicolor GISH (McGISH) analyses demonstrated that the three octoploid Trititrigia possess 42 wheat chromosomes and 14 Th. intermedium chromosomes. The 14 alien (Th. intermedium) chromosomes belong to a mixed genome consisting of J-, JS- and St-genome chromosomes rather than a single J, JS or St genome. Different types of chromosomal structural variation were also detected in the 1A, 6A, 6B, 2D and 7D chromosomes via FISH, McGISH and molecular marker analysis. The identity of the alien chromosomes and the variationes in the wheat chromosomes in the three Trititrigia octoploids were also different. Conclusions The wheat-Th. intermedium partial amphiploids possess 14 alien chromosomes which belong to a mixed genome consisting of J-, JS- and St- chromosomes, and 42 wheat chromosomes with different structural variations. These accessions could be used as genetic resources in wheat breeding for the transfer of disease and pest resistance genes from Th. intermedium to common wheat.

Evaluation of resistance to wheat stem rust and identification of resistance genes in wheat lines from Heilongjiang province

Wheat stem rust, caused by Puccinia graminis f. sp. tritici, (Pgt) is a devastating disease in wheat production. The disease has been effectively controlled since the 1970s due to the widespread use of the Sr31 resistance gene. However, Sr31 has lost its effectiveness following the emergence and spread of the Ug99 race variants. Therefore, there is an urgent global effort to identify new germplasm resources effective against those races. In this study, the resistance to Pgt of 95 wheat advance lines from Heilongjiang Province was evaluated using three predominant races of Pgt, 21C3CTTTM, 34C0MKGSM, and 34C3MTGQM, in China at the seedling and adult plant stage. The presence of 6 Sr genes (Sr2, Sr24, Sr25, Sr26, Sr31, and Sr38) was evaluated using linked molecular markers. The results showed that 86 (90.5%) wheat lines had plant stage resistance to all three races. Molecular marker analysis showed that 24 wheat lines likely carried Sr38, 15 wheat lines likely carried Sr2, 11 wheat lines likely carried Sr31, while none of the wheat lines carried Sr24, Sr25, or Sr26. Furthermore, six out of the 95 wheat lines tested carried both Sr2 and Sr38, three contained both Sr31 and Sr38, and two wheat lines contained both Sr2 and Sr31. Wheat lines with known Sr genes may be used as donor parents for further breeding programs to provide resistance to stem rust.

Karyotyping Dasypyrum breviaristatum chromosomes with multiple oligonucleotide probes reveals the genomic divergence in Dasypyrum

The perennial species <i>Dasypyrum breviaristatum</i> (genome V^b) contains many potentially valuable genes for the improvement of common wheat. Construction of a detailed karyotype of <i>D. breviaristatum</i> chromosomes will be useful for the detection of <i>Dasypyrum</i> chromatin in wheat background. We established the standard karyotype of 1V^b-7V^b chromosomes through non-denaturing fluorescence <i>in situ</i> hybridization (ND-FISH) technique using 28 oligonucleotide probes from the wheat-<i>D. breviaristatum</i> partial amphiploid TDH-2 (AABBV^bV^b) and newly identified wheat-<i>D. breviaristatum</i> disomic translocation and addition lines D2138 (6V^bS.2V^bL), D2547 (4V^b) and D2532 (3V^bS.6V^bL) by comparative molecular marker analysis. The ND-FISH with multiple oligo probes were conducted on the durum wheat-<i>D. villosum</i> amphiploid TDV-1 and large karyotype differences between <i>D. breviaristatum</i> and <i>D. villosum</i> was revealed. These ND-FISH probes will be valuable for screening the wheat-<i>Dasypyrum</i> derivative lines for chromosome identification, and newly developed wheat-<i>D. breviaristatum</i> addition lines may broaden the gene pool of wheat breeding. The differences between <i>D. villosum</i> and <i>D. breviaristatum</i> chromosomes revealed by ND-FISH will help us understand evolutionary divergence of repetitive sequences within the genus <i>Dasypyrum</i>.

Generation and molecular marker and cytological characterization of wheat – Secale strictum subsp. anatolicum derivatives

Cereal rye and its wild forms are important sources of genetic diversity for wheat breeding due to their resistances to biotic and abiotic stresses. Secale strictum subsp. anatolicum (Boiss.) K. Hammer (SSA) is a weedy relative of cultivated rye, S. cereale. Meiotic chromosome pairing in F1 hybrids of SSA and S. cereale reveals strong genomic affinity between the two genomes. A study of the transferability of S. cereale sequence-based markers to SSA and hexaploid triticale demonstrated their applicability for tracing SSA chromatin in wheat. The transferability of the markers was over 80% from homoeologous groups 1, 2, and 3, and greater than 70% from groups 4 to 7. This study focused on the generation and molecular and cytogenetic characterization of wheat–SSA alien derivatives. Twelve were identified using combinations of non-denaturing fluorescence in situ hybridization (ND-FISH), genomic in situ hybridization (GISH), and molecular marker analysis. All SSA chromosomes, except 3Ra and 6Ra, were transferred to wheat either in the form of monosomic additions (MA), mono-telosomic additions (MtA), double-mono-telosomic additions (dMtA), or double-monosomic additions (dMA). The germplasm developed in this study will help to enhance the genetic base of wheat and facilitate molecular breeding of wheat and triticale.

Seed genetic purity testing of F1 Benincasa hispida var. chieh-qua hybrids using SSR molecular marker analysis

To ensure that farmers can access high-quality seeds, it is essential to find a simple, rapid and accurate method to assess seed purity. In recent years, heterosis in chieh-qua has been widely applied to production. Using the whole genome sequence of chieh-qua, we designed simple sequence repeat (SSR) primers specific for chieh-qua. The parental lines of nine hybrids were screened using 200 SSR primers, seven of which exhibited polymorphisms. The bands were clear, stable and reproducible. We found dominant and co-dominant bands between the parents of the nine hybrids. The seven pairs of SSR primers were successfully used to assess genetic purity of the nine chieh-qua hybrids. The SSR molecular marker purity assessment results were consistent with the results obtained from a field grow-out test (GOT). However, the use of SSR markers provided a more accurate, reliable and faster method for seed purity testing than the GOT. We propose using SSR molecular marker technology to assess the genetic purity of chieh-qua hybrid seeds. With this method, the seed quality can be determined faster, which may help to accelerate the chieh-qua breeding process.

Agronomic and molecular evaluation of rice lines in a breeding program

Obtaining new and improved varieties of rice requires long and complex plant breeding programs. The early detection of desirable characteristics is a complex process, especially when seeking to improve yield, as the interaction between the environment and plants may hinder selection in early generations considerably. Techniques that facilitate the selection of plants with desirable characteristics in early generations are highly valuable to plant breeders. An indirect selection method in early generations of rice was examined by principal component analysis of performance supported by field tests with a honeycomb design. This study used double haploid lines of rice obtained by crossing two rice varieties, namely ‘Benisants’ and ‘Gigante Vercelli’. This method was compared to indirect selection using genomic tools such as high-throughput molecular marker analysis. The main factors that can be used in indirect selection have been selected by principal component analysis. The model resulting from the phenological evaluation and principal component analysis with six selected variables explained 98.73% of the total variability of yield. The variable that contributes the most to the model is the Harvest Index. The best selected lines provided 32% and 43% higher yield values than the parentals and match the results from indirect selection with molecular markers.