Genome-Wide Association Analysis of Stable Stripe Rust Resistance Loci in a Chinese Wheat Landrace Panel Using the 660K SNP Array

Stripe rust (caused by Puccinia striiformis f. sp. tritici) is one of the most severe diseases affecting wheat production. The disease is best controlled by developing and growing resistant cultivars. Chinese wheat (Triticum aestivum) landraces have excellent resistance to stripe rust. The objectives of this study were to identify wheat landraces with stable resistance and map quantitative trait loci (QTL) for resistance to stripe rust from 271 Chinese wheat landraces using a genome-wide association study (GWAS) approach. The landraces were phenotyped for stripe rust responses at the seedling stage with two predominant Chinese races of P. striiformis f. sp. tritici in a greenhouse and the adult-plant stage in four field environments and genotyped using the 660K wheat single-nucleotide polymorphism (SNP) array. Thirteen landraces with stable resistance were identified, and 17 QTL, including eight associated to all-stage resistance and nine to adult-plant resistance, were mapped on chromosomes 1A, 1B, 2A, 2D, 3A, 3B, 5A, 5B, 6D, and 7A. These QTL explained 6.06–16.46% of the phenotypic variation. Five of the QTL, QYrCL.sicau-3AL, QYrCL.sicau-3B.4, QYrCL.sicau-3B.5, QYrCL.sicau-5AL.1 and QYrCL.sicau-7AL, were likely new. Five Kompetitive allele specific PCR (KASP) markers for four of the QTL were converted from the significant SNP markers. The identified wheat landraces with stable resistance to stripe rust, significant QTL, and KASP markers should be useful for breeding wheat cultivars with durable resistance to stripe rust.

SNP-based Genetic Structure of Tunisian Durum Wheat Landraces and Distribution of the Resistance to Septoria Tritici Blotch

Background: Septoria tritici blotch (STB) has marked durum wheat production worldwide. This fungal disease is until today a challenge for farmers, researchers and breeders all united in the aim of reducing its damage and improving wheat resistance. Tunisian durum wheat landraces were reported to be valuable genetic resources for resistance to biotic and abiotic stresses and are therefore prominently deployed in breeding programs to develop new varieties adapted to fungal diseases as STB and to climate change constraints overall.Results: A total of 366 local durum wheat accessions were assessed for resistance to two virulent Tunisian isolates of Zymoseptoria tritici Tun06 and TM220 under field conditions. Population structure analysis of the durum wheat accessions, performed with 286 polymorphic SNPs (PIC >0.3) covering the entire genome, identified three genetic subpopulations (GS1, GS2 and GS3) with 22% of admixed genotypes. Interestingly, all of the resistant genotypes were among GS2 or admixed with GS2. Conclusions: This study revealed the population structure and the genetic distribution of the resistance to Z. tritici in the Tunisian durum wheat landraces. The grouping pattern of accessions appear to be associated, to some extent, with the geographical pattern of the landraces. We suggested that GS2 accessions were mostly introduced from eastern Mediterranean populations, unlike GS1 and GS3 that originated from the west. Resistant GS2 accessions belonged to landraces Taganrog, Sbei glabre, Richi, Mekki, Badri, Jneh Khotifa and Azizi. Furthermore, we suggested that admixture contributed to transmit STB resistance from GS2 resistant landraces to initially susceptible landraces such as Mahmoudi (GS1), but also resulted in the loss of resistance in the case of GS2 suscpetible Azizi and Jneh Khotifa accessions.

Genome-wide Association Study of Kernel Black Point Resistance in Chinese Wheat Landraces

Black point (BP) disease of wheat has become a noticeable problem in China. The symptoms are brown to black in color around the wheat kernel embryo or in the endosperm, resulting in a significant reduction of wheat grain quality. Here, we evaluated 272 Chinese wheat landraces for BP reaction and performed a genome-wide association study (GWAS) to identify BP resistance quantitative trait loci (QTL) in five field environments without artificial inoculation. The BP incidence data showed continuous distributions and had low to moderate correlations between environments (r = 0.094 – 0.314). Among the 272 landraces, 11 had 0.1% to 4.9%, 144 had 5% to 14.9%, and 100 had 15% to 29.9%, and 17 had over 30% incidence. We found three resistant accessions: WH094 (3.33%), AS661463 (2.67%), and AS661231 (2.67%), which can be used in breeding programs to enhance BP resistance. We identified 11 QTL, which explained 8.22% to 10.99% phenotypic BP variation and mapped them to eight wheat chromosomes. Three of the QTL were novel. The molecular markers for the BP resistance could facilitate molecular breeding for developing BP resistant cultivars.

Exploring the legacy of Central European historical winter wheat landraces

Historical wheat landraces are rich sources of genetic diversity offering untapped reservoirs for broadening the genetic base of modern varieties. Using a 20K SNP array, we investigated the accessible genetic diversity in a Central European bread wheat landrace collection with great drought, heat stress tolerance and higher tillering capacity. We discovered distinct differences in the number of average polymorphisms between landraces and modern wheat cultivars, and identified a set of novel rare alleles present at low frequencies in the landrace collection. The detected polymorphisms were unevenly distributed along the wheat genome, and polymorphic markers co-localized with genes of great agronomic importance. The geographical distribution of the inferred Bayesian clustering revealed six genetically homogenous ancestral groups among the collection, where the Central European core bared an admixed background originating from four ancestral groups. We evaluated the effective population sizes (Ne) of the Central European collection and assessed changes in diversity over time, which revealed a dramatic ~ 97% genetic erosion between 1955 and 2015.

In-Field Comparative Study of Landraces vs. Modern Wheat Genotypes under a Mediterranean Climate

The Near East climate ranges from arid to a Mediterranean, under which local wheat landraces have been grown for over millennia, assumingly accumulating a unique repertoire of genetic adaptations. In the current study, we subjected a subset of the Israeli Palestinian Landraces (IPLR) collection (n = 19: durum and bread wheat landraces, modern wheat cultivars, and landraces mixtures) to full-field evaluation. The multifield experiment included a semiarid site (2018–2019, 2019–2020) under low (L) and high (H) supplementary irrigation, and a Mediterranean site (2019–2020). Water availability had a major impact on crop performance. This was reflected in a strong discrimination between environments for biomass productivity and yield components. Compared to landraces, modern cultivars exhibited significantly higher grain yield (GY) across environments (+102%) reflecting the effect of the Green Revolution. However, under the Gilat19 (L) environment, this productivity gap was significantly reduced (only +39%). Five excelling landraces and the durum mix exhibited good agronomic potential across all trails. This was expressed in relatively high GY (2.3–2.85 t ha−1), early phenology (86–96 days to heading) and lodging resistance. Given the growing interest of stakeholders and consumers, these might be considered future candidates for the local artisanal wheat grain market. Yet, this step should be taken only after establishing an adjustable field management protocol.

Effects of foliar application of micronutrients on concentration and bioavailability of zinc and iron in wheat landraces and cultivars

Foliar application of micronutrient is a rapid and promising strategy to enhance the concentration and bioavailability of micronutrients in wheat grain. To explore the effects of foliar application of micronutrients on the concentration and bioavailability of zinc and iron in grain in wheat cultivars and landraces, field experiments were carried out using 65 wheat cultivars and 28 landraces to assess the effects of foliar application of zinc (iron) on phytic acid concentrations, zinc (iron) concentrations and their molar ratios. The results indicated that mean grain zinc concentration of landraces (44.83 mg kg−1) was 11.13% greater than that of cultivars (40.34 mg kg−1) on average across seasons, while grain iron concentration did not differ significantly between landraces (41.00 mg kg−1) and cultivars (39.43 mg kg−1). Foliar zinc application significantly improved the concentration and bioavailability of zinc in grains in both cultivars and landraces, while landraces had almost two-fold more increase in grain zinc and also greater improvement in zinc bioavailability compared to cultivars. While foliar iron application did not significantly affect iron concentration and bioavailability in grains in either cultivars or landraces. Our study showed that, with foliar application of zinc but not iron, wheat landraces had better performance than cultivars in terms of the increases in both concentration and bioavailability of micronutrient in grains.

SNP-Based Genetic Structure of Tunisian Durum Wheat Landraces and Distribution of the Resistance to Septoria Tritici Blotch

Background: Septoria tritici blotch (STB) has marked durum wheat production worldwide. This fungal disease is until today a challenge for farmers, researchers and breeders all united in the aim of reducing its damage and improving wheat resistance. Tunisian durum wheat landraces were reported to be valuable genetic resources for resistance to biotic and abiotic stresses and are therefore prominently deployed in breeding programs to develop new varieties adapted to fungal diseases as STB and to climate change constraints overall.Results: A total of 366 local durum wheat accessions were assessed for resistance to two virulent Tunisian isolates of Zymoseptoria tritici Tun06 and TM220 under field conditions. Population structure analysis of the durum wheat accessions, performed with 286 polymorphic SNPs (PIC >0.3) covering the entire genome, identified three genetic subpopulations (GS1, GS2 and GS3) with 22% of admixed genotypes. Interestingly, all of the resistant genotypes were among GS2 or admixed with GS2. Conclusions: This study revealed the population structure and the genetic distribution of the resistance to Z. tritici in the Tunisian durum wheat landraces. The grouping pattern of accessions appear to be associated, to some extent, with the geographical pattern of the landraces. We suggested that GS2 accessions were mostly introduced from eastern Mediterranean populations, unlike GS1 and GS3 that originated from the west. Resistant GS2 accessions belonged to landraces Taganrog, Sbei glabre, Richi, Mekki, Badri, Jneh Khotifa and Azizi. Furthermore, we suggested that admixture contributed to transmit STB resistance from GS2 resistant landraces to initially susceptible landraces such as Mahmoudi (GS1), but also resulted in the loss of resistance in the case of GS2 suscpetible Azizi and Jneh Khotifa accessions.