SNP-based association analysis for seedling traits in durum wheat (Triticum turgidum L. durum (Desf.))

Drought-Tolerance QTLs Associated with Grain Yield and Related Traits in Spring Bread Wheat

The present research aims to identify the efficient combination of drought-tolerance selection criteria and associated quantitative trait loci. A panel of 197 bread wheat genotypes was evaluated for yield- and drought-tolerance-related traits in two environments (favorable and semiarid) for 2 years (2015-2016). Grain number, biomass, number of fertile spikes per plant and ground cover exhibited a significant correlation with grain yield and constitute potential secondary selection criteria for yield under drought conditions. About 73 significant marker-trait associations were detected along various chromosomal positions. The markers "wsnp_Ex_Rep_c67786_66472676" and "ExcalibuR_c24593_1217" exhibited important genetic gains associated with yield increase under drought (11 and 7%, respectively). The markers "KukRi_c94792_127" and "wsnp_Ex_c298_580660" showed a significant correlation with grain yield, biomass and grain number and were associated with a significant increase in yield performance at the semiarid site (+6 and +7%, respectively). The ground cover was found associated with grain yield and biomass through the markers "wsnp_Ex_Rep_c67786_66472676" (+11%) and "KukRi_c49927_151" (+10%). One marker "TduRuM_contig25432_1377" on chromosome 5B at 20 cM was consistently correlated with the number of fertile spikes across both environments. Further research should be considered to validate the efficiency of these markers to undertake selection for drought tolerance under various environments and genetic backgrounds.

SNP-based association study of kernel architecture in a worldwide collection of durum wheat germplasm

Durum wheat, genetic resource with favorable alleles is considered as natural gene pool for wheat breeding. Kernel size and weight are important factors affecting grain yield in crops. Here, association analysis was performed to dissect the genetic constitution of kernel-related traits in 150 lines collected from 46 countries and regions using a set of EST-derived and genome-wide SNP markers with five consecutive years of data. Total 109 significant associations for eight kernel-related traits were detected under a mix linear model, generating 54 unique SNP markers distributed on 13 of 14 chromosomes. Of which, 19 marker-trait associations were identified in two or more environments, including one stable and pleiotropic SNP BE500291_5_A_37 on chromosome 5A correlated with six kernel traits. Although most of our SNP loci were overlapped with the previously known kernel weight QTLs, several novel loci for kernel traits in durum were reported. Correlation analysis implied that the moderate climatic variables during growth and development of durum are needed for the large grain size and high grain weight. Combined with our previous studies, we found that chromosome 5A might play an important role in durum growth and development.

Genome-Wide Association Mapping of Prostrate/Erect Growth Habit in Winter Durum Wheat

By selecting for prostrate growth habit of the juvenile phase of the cycle, durum wheat cultivars could be developed with improved competitive ability against weeds, and better soil coverage to reduce the soil water lost by evaporation. A panel of 184 durum wheat (Triticum turgidum subsp. durum) genotypes, previously genotyped with DArT-seq markers, was used to perform association mapping analysis of prostrate/erect growth habit trait and to identify candidate genes. Phenotypic data of plant growth habit were recorded during three consecutive growing seasons (2014–2016), two different growth conditions (field trial and greenhouse) and two sowing periods (autumn and spring). Genome-wide association study revealed significant marker-trait associations, twelve of which were specific for a single environment/year, 4 consistent in two environments, and two MTAs for the LSmeans were identified across all environments, on chromosomes 2B and 5A. The co-localization of some MTAs identified in this study with known vernalization and photoperiod genes demonstrated that the sensitivity to vernalization and photoperiod response are actually not only key components of spring/winter growth habit, but they play also an important role in defining the magnitude of the tiller angle during the tillering stage. Many zinc-finger transcription factors, such as C2H2 or CCCH-domain zinc finger proteins, known to be involved in plant growth habit and in leaf angle regulation were found as among the most likely candidate genes. The highest numbers of candidate genes putatively related to the trait were found on chromosomes 3A, 4B, 5A and 6A. Moreover, a bioinformatic approach has been considered to search for functional ortholog genes in wheat by using the sequence of rice and barley tiller angle-related genes. The information generated could be used to improve the understanding of the mechanisms that regulate the prostrate/erect growth habit in wheat and the adaptive potential of durum wheat under resource-limited environmental conditions.

Associations of canopy leaf traits with SNP markers in durum wheat (Triticum turgidum L. durum (Desf.))

The canopy leaves including the top three, i.e., the flag, the 2nd and 3rd from the top, are important for photosynthesis and grain yield of wheat. Molecular markers associated with traits of these leaves should be helpful for the high-yielding breeding. In this study, 1366 single nucleotide polymorphisms (SNP) markers covering the whole genome of durum wheat were used to genotype 150 cultivars collected from 46 countries and regions in the world. Leaf length, leaf width and chlorophyll content of the top three leaves were measured, respectively, in three consecutive years. Association analyses were performed on the leaf traits and SNP markers. A total of 120 SNP marker associations were detected on 13 of the 14 chromosomes. Among these markers, 83 were associated with the canopy leaf traits, 10 with 1000-grain weight, and 29 with kernel number per spike. This study is helpful for better understanding the potential and genetic basis of functional leaves, and facilitates pyramiding of the favorable alleles using marker assisted selection for ideal plant-type and high photosynthesis efficiency in durum wheat breeding.

Detection of QTLs for seedling characteristics in barley (Hordeum vulgare L.) grown under hydroponic culture condition

BACKGROUND

Seedling characteristics play significant roles in the growth and development of barley (Hordeum vulgare L.), including stable stand establishment, water and nutrients uptake, biotic resistance and abiotic stresses, and can influence yield and quality. However, the genetic mechanisms underlying seedling characteristics in barley are largely unknown and little research has been done. In the present work, 21 seedling-related characteristics are assessed in a barley double haploid (DH) population, grown under hydroponic conditions. Of them, leaf age (LAG), shoot height (SH), maximum root length (MRL), main root number (MRN) and seedling fresh weight (SFW) were investigated at the 13th, 20th, 27th, and 34th day after germination. The objectives were to identify quantitative trait loci (QTLs) underlying these seedling characteristics using a high-density linkage map and to reveal the QTL expression pattern by comparing the QTLs among four different seedling growth stages.

RESULTS

A total of 70 QTLs were distributed over all chromosomes except 4H, and, individually, accounted for 5.01%-77.78% of phenotypic variation. Out of the 70 detected QTLs, 23 showed a major effect on 14 seedling-related characteristics. Ten co-localized chromosomal regions on 2H (five regions), 3H (two regions) and 7H (three regions) involved 39 QTLs (55.71%), each simultaneously influenced more than one trait. Meanwhile, 9 co-localized genomic regions involving 22 QTLs for five seedling characteristics (LAG, SH, MRL, MRN and SFW) at the 13th, 20th, 27th and 34th day-old seedling were common for two or more growth stages of seedling. QTL in the vicinity of Vrs1 locus on chromosome 2H with the favorable alleles from Huadamai 6 was found to have the largest main effects on multiple seedling-related traits.

CONCLUSIONS

Six QTL cluster regions associated with 16 seedling-related characteristics were observed on chromosome 2H, 3H and 7H. The majority of the 29 regions identified for five seedling characteristics were selectively expressed at different developmental stages. The genetic effects of 9 consecutive expression regions displayed different developmental influences at different developmental stages. These findings enhanced our understanding of a genetic basis underlying seedling characteristics in barley. Some QTLs detected here could be used for marker-assisted selection (MAS) in barley breeding.