Durum wheat (Triticum turgidum L. var. durum) root system response to drought and salt stresses and genetic characterization for root-related traits

Abiotic stresses such as drought and salt are significant threats to crop productivity. The root system adaptation and tolerance to abiotic stresses are regulated by many biochemical reactions, which create a complex and multigenic response. The present study aims to evaluate the diversity of root responses to cyclic abiotic stress in three modern durum wheat varieties and one hydric stress-tolerant landrace in a pot experiment from seedling to more advanced plant development stages. The genotypes responded to abiotic stress during the whole experiment very differently, and at the end of the experiment, nine out of the 13 traits for the landrace J. Khetifa were significantly higher than other genotypes. Moreover, single sequence repeat (SSR) genetic analysis revealed high polymorphism among the genotypes screened and interesting private alleles associated with root system architecture traits. We propose that the markers used in this study could be a resource as material for durum wheat breeding programs based on marker-assisted selection to increase the vegetal material with high drought and salt stress tolerance and to identify candidates with strong early vigor and efficient root systems. This study provides appropriate genetic materials for marker-assisted breeding programs as well as a basic study for the genetic diversity of root traits of durum wheat crops.

Exploring genetic diversity and ascertaining genetic loci associated with important fruit quality traits in apple (Malus × domestica Borkh.)

Genetic diversity is the primary source of variability in any crop improvement program, and the diverse germplasm of any crop species represents an important genetic resource for gene or allele mining to meet future needs. Huge genetic and phenotypic diversity is present in the apple gene pool, even though, breeding programs have been mainly focused on a few traits of interests, which have resulted in the reduction of the diversity in the cultivated lines of apple. Therefore, the present study was carried out on 70 diverse apple genotypes with the objective of analyzing the genetic diversity and to identify the genetic loci associated with important fruit quality traits. A total of 140 SSR primers were used to characterize the 70 genotypes of apples, out of which only 88 SSRs were found to be polymorphic. The PIC values varied from 0.03 to 0.75. The value of MI, EMR, and RP varied from 0.03 to 3.5, 0.5 to 5.0, and 1.89 to 6.74, respectively. The dendrogram and structure analysis divided all the genotypes into two main groups. In addition to this, large phenotypic variability was observed for the fruit quality traits under study indicated the suitability of the genotypes for association studies. Altogether 71 novel MTAs were identified for 10 fruit quality traits, of which 15 for fruit length, 15 for fruit diameter, 12 for fruit weight, 2 for total sugar, 2 for TSS, 4 for reducing sugar, 5 for non-reducing sugar, 5 for fruit firmness, 5 for fruit acidity and 6 for anthocyanin, respectively. Consistent with the physicochemical evaluation of traits, there was a significant correlation coefficient among different fruit quality characters, and many common markers were found to be associated with these traits (fruit diameter, length, TSS, total sugar, acidity and anthocyanin, respectively) by using the different modeling techniques (GLM, MLM). The inferred genetic structure, diversity pattern and the identified MTAs will be serving as resourceful grounds for better predictions and understanding of apple genome towards efficient conservation and utilization of apple germplasm for facilitating genetic improvement of fruit quality traits. Furthermore, these findings also suggested that association mapping could be a viable alternative to the conventional QTL mapping approach in apple.

Graphic abstract

Supplementary Information

The online version contains supplementary material available at 10.1007/s12298-023-01382-w.

Screening and Evaluation of Excellent Blackberry Cultivars and Strains Based on Nutritional Quality, Antioxidant Properties, and Genetic Diversity

To screen and evaluate excellent blackberry cultivars and strains, 17 indexes of plant growth and fruit horticultural and nutritional characteristics were measured, 20 simple sequence repeat (SSR) markers were analyzed, the fingerprints of 23 blackberry cultivars and strains were constructed, and the processing characteristics of 10 excellent cultivars and strains were evaluated. The results showed that 'Chester' and 'Shuofeng' had the highest plant yield (6.5 kg per plant), of which the 'Chester' fruit also had the highest hardness (2.78 kg/cm2). 'Kiowa' had the highest single fruit weight (10.43 g). '10-5n-2' had the highest total anthocyanin content (225.4 mg/100 g FW) and total polyphenol content (3.24 mg/g FW), but a low plant yield. These results suggest that 'Shuofeng' and 'Chester' are the top two blackberry cultivars planted in Nanjing, with the best growth and comprehensive quality. Moreover, a total of 119 alleles were detected with an average number of 6 alleles per locus. The polymorphism information content (PIC) was 0.374~0.844, with an average of 0.739, indicating a high genetic diversity among the 23 blackberry cultivars and strains. This study provides insight into the plant growth, fruit characteristics and genetic diversity of the 23 blackberry cultivars and strains, and is thus conducive to the protection and utilization of blackberry cultivars and strains.

Development of novel polymorphic microsatellite markers for Picea brachytyla

BACKGROUND

Picea brachytyla is a unique tree species in China. Due to being extensively exploited in the past, it is listed as Vulnerable in the IUCN Red List. It is mainly distributed across the Hengduan and Daba-Qinglin mountains and has been found in other areas including Sichuan Province and Qinghai Province, China. Microsatellites, or simple sequence repeats (SSRs), are widely used in correlational studies of genetic protection. Few markers have been developed for P. brachytyla because of the small number of trees and scholarly resources available for study.

METHODS AND RESULTS

The genomic DNA of P. brachytyla was sequenced using the DNBSEQ platform, and unigenes were obtained after assembly and deredundancy. Of the 100 primer pairs screened, we isolated 10 useful microsatellite loci from P. brachytyla genes. The observed and expected heterozygosity values ranged from 0.173 (P24) to 0.788 (P79; mean 0.469) and 0.199 (P87) to 0.911 (P79; mean 0.700), respectively. Polymorphism-information content (PIC) ranged from 0.190 (P84) to 0.904 (P79; mean 0.666). Only P84 and P72 were in a Hardy-Weinberg equilibrium (P > 0.05) in the different P. brachytyla populations. All the levels of linkage disequilibrium (LD) were high for the 10 SSR loci indicating that there were no autocorrelations among the 10 SSR loci.

CONCLUSIONS

The novel polymorphic microsatellite markers showed high polymorphism for P. brachytyla. These polymorphic microsatellites can provide a basis for future conservation and genetic research on this rare plant species.

Assessment of genetic diversity of pumpkins (Cucurbita spp.) from western Kenya using SSR molecular markers

Pumpkins (Cucurbita spp.) are among most neglected and underutilized crops cultivated for food and medicine. The major constraint to pumpkin production is lack of genetically improved seeds. The current study was aimed at evaluating the genetic diversity of pumpkins from eight counties in western Kenya using five SSR markers. Seeds were extracted from pumpkin fruits, dried and planted on plastic trays for 4 weeks. DNA was isolated from young leaves using CTAB method and amplified. The samples were genotyped using an ABI 3730 genetic analyzer and the allelic data analyzed using Power Marker V 3.25, DARwin V 6.0.12 and GenAIEx V 6.41software. The five SSR loci were polymorphic with a total of 33 alleles and a mean PIC value of 0.534. The gene diversity and observed heterozygosity was 0.796-0.329 and 0.967-0.164, respectively. Most of genetic variations were found within and among individual samples rather than among counties, with samples of some counties having private alleles. Based on the inbreeding coefficient (F), there was outbreeding in pumpkins from Kakamega county (F = - 0.282) and inbreeding in pumpkins from Kisii, Bungoma and Nyamira counties (F = 0.500, 0.409 and 0.286 respectively). The findings of this study suggest that genetic variation and distribution of pumpkins in western Kenya was due to monocropping and intercropping farming systems, trading of pumpkins in markets and exchange of seeds among local farmers rather than geographical and climatic differences.

Identification of leaf rust resistance genes Lr34 and Lr46 in common wheat (Triticum aestivum L. ssp. aestivum) lines of different origin using multiplex PCR

Leaf rust caused by the fungus Puccinia recondita f. sp. tritici is one of the most dangerous diseases of common wheat. Infections caused by fungal pathogens reduce the quantity and quality of yields of many cereal species. The most effective method to limit plant infection is to use cultivars that show rust resistance. Genetically conditioned horizontal-type resistance (racial-nonspecific) is a desirable trait because it is characterized by more stable expression compared to major (R) genes that induce racially specific resistance, often overcome by pathogens. Horizontal resistance is conditioned by the presence of slow rust genes, which include genes Lr34 and Lr46. This study aimed to identify markers linked to both genes in 64 common wheat lines and to develop multiplex PCR reaction conditions that were applied to identify both genes simultaneously. The degree of infestation of the analyzed lines was also assessed in field conditions during the growing season of 2017 and 2018. Simple sequence repeat anchored-polymerase chain reaction (SSR-PCR) marker csLV was identified during analysis in line PHR 4947. The presence of a specific sequence has also been confirmed in multiplex PCR analyses. In addition to gene Lr34, gene Lr46 was identified in this genotype. Lines PHR 4947 and PHR 4819 were characterized by the highest leaf rust resistance in field conditions. During STS-PCR analyses, the marker wmc44 of gene Lr46 was identified in most of the analyzed lines. This marker was not present in the following genotypes: PHR 4670, PHR 4800, PHR 4859, PHR 4907, PHR 4922, PHR 4949, PHR 4957, PHR 4995, and PHR 4997. The presence of a specific sequence has also been confirmed in multiplex PCR analyses. Genotypes carrying the markers of the analyzed gene showed good resistance to leaf rust in field conditions in both 2017 and 2018. Research has demonstrated that marker assisted selection (MAS) and multiplex PCR techniques are excellent tools for selecting genotypes resistant to leaf rust.

[Association analysis of phenotypic traits of alkaloid content in Sophora alopecuroides with SSR molecular markers]

To further study and fully exploit the medicinal plant Sophora alopecuroides, the molecular markers related with the phenotypic traits of alkaloid content in S. alopecuroides should be detected. In this study, SSR molecular markers were used to analyze the genetic diversity and genetic structure of 23 S. alopecuroides populations, in combination with the association analysis between molecular markers and the alkaloid contents. The results showed that P, H, I, G_(st) and N_m values were 40.10%, 0.335 3, 0.504 5, 0.433 7 and 0.625 9 respectively, in 23 S. alopecuroides populations. This indicated that there was less gene exchange and higher genetic differentiation among different S. alopecuroides populations. The results of SSR unweighted pair-group method with arithmetic means(UPGMA) cluster showed that the S. alopecuroides populations relationship from Xinjiang was far from the populations of other regions, but the populations of S. alopecuroides from Gansu, Inner Mongolia and Qinghai were closely relevant to those from Ningxia. The 23 populations were further divided into 2 genetic subpopulations by the population structure analysis. Through association analysis, a total of 26 loci in 13 SSR markers were found to be significantly associated(P<0.005)with the content of MA, OMA, SC and OSC, and the rate of explanation on the phenotype variance of related markers ranged from 36.45% to 77.93%. Among the locus, 1 each were related with MA and OSC content at interpretation rate reached as high as 50% with high threshold(P<0.000 1). These results could provide support for the discovery of important genes in the alkaloid biosynthetic and metabolic pathway of S. alopecuroides.

Identification of Leaf Rust Resistance Genes in Selected Wheat Cultivars and Development of Multiplex PCR

Ten leading wheat cultivars originating from the Plant Breeding and Acclimatization Institute (IHAR) - National Research Institute (Poland) and the Department of Gene Bank (Czech Republic) were used to establish a field experiment in 2017 and 2018 at the Dłoń Experimental Farm. The analyzed wheat genotypes were characterized by diversified field resistance to leaf rust. Jubilatka, Thatcher and Sparta were the most resistant cultivars in field conditions in both 2017 and 2018. The aim of the work was to identify the Lr11, L13, Lr16 and Lr26 genes encoding resistance to leaf rust using molecular SSR markers (wmc24, wmc261, Xgwm630, Xwmc764 and P6M12) and to develop multiplex PCR conditions to accelerate identification of these genes. Markers of three leaf rust resistance genes have been identified simultaneously in these cultivars. Jubilatka, Thatcher and Sparta cultivars may serve as a good source of the analyzed leaf rust resistance genes. In addition, multiplex PCR conditions have been developed for the simultaneous identification of the Lr11 and Lr16 and Lr11 and Lr26 gene pairs.