Breeding for salt tolerance in wheat: The contribution of carbon isotopic signatures

Use of low-quality water for supplemental irrigation is expected to become soon a common practice in the Mediterranean area, where durum wheat is the main cultivated cereal. Breeding for salt stress tolerance may contribute to the improvement of wheat resilience to irrigation with brackish water. Various traits can be considered as indicators of salt stress tolerance, which include agronomical and physiological criteria. However, the complexity of salinity tolerance mechanisms, the G × E interaction and the lack of correlation between controlled and open field conditions causes uncertainty in the selection process. The present review highlights the main advantages and limitations of different agronomical and physiological traits used in screening for salt stress tolerance in wheat. Special focus is given to carbon and nitrogen isotope discrimination, that remains a bottleneck in breeding for salt stress tolerance. The use of different statistical tools to analyse data related to salt stress tolerance is also discussed in this review.

Study on fine mapping of QTL for juice yield traits of sweet sorghum (Sorghum dochna)

The stem juice yield is a key factor that influences both the biological and economic production of sweet sorghum [Sorghum dochna (Forssk.) Snowden]. To elucidate upon the genetic basis of the stem juice yield, an F₅ population developed from a cross between the low juice yielding Xinliang52 (XL52) and high juice yielding W455 lines, were used in a quantitative trait locus (QTL) analysis. A main effect of the QTL controlling stem juice yield was separated with an SSR marker called Xtxp97, which explained 46.7% of the phenotypic variance. In addition, F₅ and F₆ populations were constructed with XL52 and W452 as the parents to further verify the QTLs, and a significant correlation was found between the juice yield trait and the Xtxp97 marker. Based on the progeny tests of 29 recombinants, QJy-sbi06 was located in a region of about 21.2 kb on chromosome 6, where a candidate gene encoding an NAC transcription factor (sobic.006G147400) was identified. Combining the different population association analysis and sequencing technology showed that XL52 inserted a 1.8 kb transposon in the NAC to directly interrupt and inactivate the juice yield gene. This study also demonstrated that the colour of the leaf midribs was controlled by a single gene and was significantly positive correlated with juiciness (r = 0.784, P < 0.01). These results could lay the foundation for map-based cloning of QJy-sbi06 and provide genes or QTLs for breeding sorghum lines with a high juice yield and quality.

Evaluation of resistance to Pseudoperonospora humuli and of the content of alpha acids and hop oils in hops of selected genetic resources of hop Humulus lupulus L.

Twenty hop genotypes were selected for the evaluation of resistance to primary and secondary Pseudoperonospora humuli infection and of alpha acid and hop oil content in the hops. From the wild hop genotypes, two from Canada and one from Belgium showed resistance. Among the registered hop varieties, the Czech varieties Kazbek and Boomerang were the most resistant. Both wild hop genotypes from Canada showed the highest content of alpha acids among the wild hop entries, namely 4% w/w. The lowest variability of the alpha acid content in the wild hop category was found in two wild hop varieties from the Caucasus, one from Austria and one from Lithuania. The highest content of hop oils was determined in two hop genotypes from Canada and two from Belgium. Wild hop genotypes from the Caucasus have the lowest variability of hop oils among the wild hop entries. Two hop genotypes from Canada and one from Belgium were selected for breeding aimed at drought resistance.

ISSR markers and morphometry determine genetic diversity and population structure in Hedera helix L.

Hedera helix L. is an invasive, but medicinally important plant. In Iran, there is no available study on the H. helix population to reveal the genetic diversity and population structure. Fifty-six individual plants belonging to nine geographical populations were collected in four provinces of Iran. High genetic diversity, polymorphisms, and a Shannon diversity index of 0.269 were detected in Mazandaran, Kandovan (Population 3). Analysis of the molecular variance indicated 40% of total genetic variation of the whole population was present in the subpopulation. A high genetic similarity (0.922) between plant Populations 5 (Kermanshah; Islamabad) and 6 (Kermanshah; Paveh) was noted. On the other hand, a low genetic similarity was observed between plant Populations 1 (Tehran; Darband) and 8 (Ardabil; Hur). The Mantel test revealed a correlation between the genetic and geographical distances. Furthermore, it demonstrated the isolation mechanism responsible for the population structure in the H. helix plant populations. The principal component analysis explained the majority of the variation in the morphological characteristics. Three components explained 87% of the variation, and the first component explained 60% of the variation. For instance, the leaf morphology showed a correlation of > 0.7 between leaf morphological and floral characters. The plant leaves and quantitative flower characteristics separated the plant populations according to the differences in length. The current results have implications for plant conservation and management.

Morpho-molecular diversity study of rice cultivars in Bangladesh

Rice is one of the frontline cereals in the world and the major cultivated crop in Bangladesh. A total of eleven simple sequence repeats (SSRs) and thirteen sequence-tagged site (STS) markers were used to characterize twenty-four rice cultivars in Bangladesh. Twenty-four markers generated 60 alleles with 2.5 alleles per locus. The average polymorphism information content (PIC) value was 0.40, while the mean value of heterozygosity, gene diversity, and major allele frequency were recorded as 0.10, 0.48 and 0.62, respectively. However, the SSR markers showed more specificity and a higher discrimination power than the STS markers. The cluster analysis displayed four major clusters with a genetic similarity coefficient value of 0.73. The morphological analyses of the grain identified that Binadhan-20 and BRRI dhan34 had the longest and the shortest seed size, respectively, with a variable correlation between the seed length, width and length/width ratio. The phenol reaction test distinguished seven cultivars as japonica and seventeen cultivars as indica or an intermediate type. All these results regarding the phenotypic data and marker information will be useful for parental selection in modern rice breeding programmes.

Disease resistance of improved MR220 lines against Pyricularia oryzae Cavara and their preliminary agronomic performance

Blast disease caused by Pyricularia oryzae is one of the most destructive fungal diseases of rice in Malaysia. Utilisation of resistant varieties is the most efficient management approach towards reducing yield losses. The line IRTP21683 with the Pi9 gene has shown strong resistance against the isolate MPO988.3 of pathotype P_0.0, the most prevalent P. oryzae pathotype in Malaysia. Crossing of IRTP21683 was undertaken with the recurrent parent MR220, a susceptible elite Malaysian rice variety, using a marker assisted backcrossing technique with two simple sequence repeat markers, RM19776 and RM7311, as the tag for the Pi9 gene. Twenty BC₃F₄ lines with the Pi9 gene were resistant when challenged with MPO 988.3. The cluster analysis based on seven agronomic parameters showed that the resistant BC₃F₄ lines could be divided into four groups, of which the members in group 1 and 2 have shown comparable or better performance than MR220. Five lines in group 1, B220PI9-3-48, B220PI9-3-76, B220PI9-3-77, B220PI9-3-79 and B220PI9-3-82 showed outstanding yield performance with early maturation.

Comparative analysis of late blight resistance R genes and their coding proteins in some potato genotypes

Late blight (LB) disease can cause potato yield losses in both Egypt and the world. Therefore, the structural analysis of resistance (R) genes responsible for LB resistance will help in understanding their functions. This work aimed to identify the variations between the dominant and recessive alleles of two genes, R3a and R8 at the nucleotide and amino acid levels in five potato genotypes. Two genes of R3a and R8 representing the broad-spectrum LB resistance were amplified by specific primers, which gave one amplicon of 194 and 220 bp of each gene, respectively. Two fragments were sequenced after purification using an ABI 3730xl System DNA Sequencer. The DNA sequence alignments of two genes, R3a and R8, were determined among five selected potato genotypes. The percentage of genetic similarity of the nucleotide sequences of the R3a and R8 genes ranged between (82–83%) and (86–87%), respectively, in comparison to the reference sequences in the nucleotide BLAST. We report on the existence of positional differences in the nucleotide sequences, and base-pair substitutions of two fragments, resulting in amino acid changes between the resistant and susceptible potato genotypes. On the other hand, the highest total number of base-pair substitutions was recorded as 16 in the recessive allele r8 of the varieties Bellini and Cara. However, the lowest number was recorded as four in the dominant allele R3a of the variety Cara. The dendrograms of the five potato genotypes were made up of phylogenetically different clusters, separate from all the other named potato accessions of the two genes. The results of this study will create a solid base for the further understanding of the mechanism of plant-pathogen interactions and supply a theoretical reference for durable resistance to late blight diseases in the potato.

A 31-bp indel localised in the 5' untranslated region of OsSUT3 affects the gene expression and rice (Oryza sativa L.) pollen development

OsSUT genes have been demonstrated to be relevant for diverse biological processes in rice. In this study, we identified the close relationship between a 31-bp insertion in a 5' untranslated region (5' UTR) of the OsSUT3 gene and higher OsSUT3 expression in rice panicles by qRT-PCR and transgenic research. Statistically significant results (P < 0.01) were found for this 31-bp insertions/deletions (indels) in the rice pollen development and other panicle traits, such as the pollen number, pollen fertility, seeding rate, and grain length. An evolution analysis showed that the proportion of the 31-bp insertion significantly increases in rice domestication. Therefore, the 31-bp Indel could be considered as a convenient molecular marker to screen more pollen and better panicle traits in rice breeding.

Isolation, sequencing of the HvnHID gene and its role in the purple-grain colour development in Tibetan hulless barley

2-hydroxyisoflavanone dehydratase (HID) plays an important role in isoflavone biosynthesis. In this study, HID was isolated from the seeds of the purple-grained Tibetan hulless barley variety Nerumuzha and the white-grained variety Kunlun 10. The HvnHID gene includes the 981 bp open reading frame and encodes a protein of 327 amino acids. It has a typical Abhydrolase_3 domain (78–306) and belongs to the carboxylesterase (CXE) family of the Abhydrolase_3 (α/β hydrolase) superfamily. There are eight nucleotide differences in the HvnHID coding sequence and two amino acid differences (one in the Abhydrolase_3 domain) between Nerumuzha and Kunlun 10. The HvnHID of hulless barley has the closest relationship with the HID in Hordeum vulgare, and the most distant relationship in Panicum hallii. At the early-mid stage of the seed colour development, the HvnHID expression levels in the purple and black seeds were significantly higher than in the white and blue ones (P < 0.01). During the seed colour development of purple-grained hulless barley, the expression of the key genes (HvnF3'H, HvnDRF, HvnANT1, and HvnGT) in the anthocyanidin biosynthetic pathway increased significantly, while the HvnHID expression decreased significantly (P < 0.01). Thus, it is likely that HvnHID negatively regulates the anthocyanidin biosynthesis. This result provides an important basis for further study of the biological functions of HvnHID in the anthocyanidin biosynthetic pathway.

Comparing the number of Iranian pomegranate genotypes based on morphological and biochemical properties

Punica granatum L. is one of the oldest known edible fruits. Numerous chemical compounds have been isolated from pomegranate seeds, juice, and peels, which have beneficial effects on human health. This study aimed to perform the physicochemical and morphological properties of twenty-four pomegranate genotypes from various provinces of Iran. Fifteen fruits of each cultivar are collected at harvest maturity in the normal ripening period for the pomegranate from the Iranian pomegranate genetic collection in Yazd, Iran. Five fruits were randomly harvested from each of four orientations of the tree, and were immediately taken to the laboratory for analysis. Three replicates were maintained for each analysis. The results indicated the highest levels of anthocyanin was observed in S783 and R633, while polyphenols in Q529, the antioxidant capacity in N755 and the total soluble solids levels in R633 and the total acidity levels were found in K477 and E336. On the other hand, the fruit weight (in S948), fruit diameter (in SH1738), crown diameter (in R533), total weight of the seeds (in S948), peel thickness (in S716), peel colour (in S948), and red juice (in S783) are significantly affected by the genotype. At a similarity of 50%, the genotypes were divided into nine sub-clusters including A, B, C, D, E, F, G, H and I. These identified genotypes can be rolled out in future breeding programmes.