High‐density molecular characterization and association mapping in Ethiopian durum wheat landraces reveals high diversity and potential for wheat breeding

Durum wheat (Triticum turgidum subsp. durum) is a key crop worldwide, and yet, its improvement and adaptation to emerging environmental threats is made difficult by the limited amount of allelic variation included in its elite pool. New allelic diversity may provide novel loci to international crop breeding through quantitative trait loci (QTL) mapping in unexplored material. Here, we report the extensive molecular and phenotypic characterization of hundreds of Ethiopian durum wheat landraces and several Ethiopian improved lines. We test 81 587 markers scoring 30 155 single nucleotide polymorphisms and use them to survey the diversity, structure, and genome‐specific variation in the panel. We show the uniqueness of Ethiopian germplasm using a siding collection of Mediterranean durum wheat accessions. We phenotype the Ethiopian panel for ten agronomic traits in two highly diversified Ethiopian environments for two consecutive years and use this information to conduct a genome‐wide association study. We identify several loci underpinning agronomic traits of interest, both confirming loci already reported and describing new promising genomic regions. These loci may be efficiently targeted with molecular markers already available to conduct marker‐assisted selection in Ethiopian and international wheat. We show that Ethiopian durum wheat represents an important and mostly unexplored source of durum wheat diversity. The panel analysed in this study allows the accumulation of QTL mapping experiments, providing the initial step for a quantitative, methodical exploitation of untapped diversity in producing a better wheat.     

The combined effect of constant water deficit and nitrogen supply on WUE, NUE and Δ13C in durum wheat potted plants

Water scarcity and nitrogen shortage are the main constraints on durum wheat productivity. This paper examines the combined effects of a constant water deficit and nitrogen supply (NS) on growth, photosynthesis, stomatal conductance (g_s) and transpiration, instantaneous and time‐integrated water use efficiency (WUE) and nitrogen use efficiency (NUE) and carbon isotope discrimination (Δ¹³C) in durum wheat genotypes grown in pots under greenhouse conditions. Three water levels (40%, 70% and 100% container capacity), two nitrogen doses (high and low N) and four genotypes were assayed in a total of 24 experimental treatments. Water and nitrogen treatments were imposed 2 weeks after plant emergence. The growth, nitrogen content and Δ¹³C of the shoot and the gas exchange in the flag leaf were determined about 2 weeks after anthesis. As expected, both water and NS had a strong positive effect on growth. However, a reduction in water supply had low effect decreasing photosynthesis and transpiration, Δ¹³C and NUE and increasing WUE. On the contrary, increasing the level of nitrogen supplied had a significant negative effect on g_s, which decreased significantly the ratio of intercellular to ambient CO₂ concentrations and Δ¹³C, and increased both instantaneous and time‐integrated WUE. In addition, a higher N level also negatively affected the instantaneous and time‐integrated NUE. The Δ¹³C of shoots correlated significantly and negatively with either instantaneous or time‐integrated measurements of WUE. Moreover, within each NS, Δ¹³C also correlated negatively with the integrated NUE. We concluded that under our experimental conditions, Δ¹³C gives information about the efficiency with which not just water but also nitrogen are used by the plant. In addition, this study illustrates that a steady water limitation may strongly affect biomass without consistent changes in WUE. The lack of effect of the different water regimes on gas exchange, WUE and Δ¹³C illustrate the importance of how stress is imposed during growth.     

Comparative response of δ13C, δ18O and δ15N in durum wheat exposed to salinity at the vegetative and reproductive stages

This study compared the performance of the stable isotope composition of carbon (δ¹³C), oxygen (δ¹⁸O) and nitrogen (δ¹⁵N) by tracking plant response and genotypic variability of durum wheat to different salinity conditions. To that end, δ¹³C, δ¹⁸O and δ¹⁵N were analysed in dry matter (dm) and the water‐soluble fraction (wsf) of leaves from plants exposed to salinity, either soon after plant emergence or at anthesis. The δ¹³C and δ¹⁸O of the wsf recorded the recent growing conditions, including changes in evaporative conditions. Regardless of the plant part (dm or wsf), δ¹³C and δ¹⁸O increased and δ¹⁵N decreased in response to stress. When the stress conditions were established just after emergence, δ¹⁵N and δ¹³C correlated positively with genotypic differences in biomass, whereas δ¹⁸O correlated negatively in the most severe treatment. When the stress conditions were imposed at anthesis, relationships between the three isotope signatures and biomass were only significant and positive within the most severe treatments. The results show that nitrogen metabolism, together with stomatal limitation, is involved in the genotypic response to salinity, with the relative importance of each factor depending on the severity and duration of the stress as well as the phenological stage that the stress occurs.     

Genetic analysis of seed size, yield and days to flowering in a chickpea recombinant inbred line population derived from a Kabuli × Desi cross

Quantitative traits, seed size, yield and days to flowering were studied in a chickpea intraspecific recombinant inbred line (RIL) population (F_6:7) derived from a Kabuli × Desi cross. The population was evaluated in two locations over 2 years. Days to flowering was also evaluated in the greenhouse under short-day conditions. Seed size was the most heritable trait (0.90), followed by days to flowering (0.36) and yield (0.14). Negative and significant correlation was found between yield and seed size in the second year where environmental homogeneity was tested by analysing the controls included in each assay. During the first year, the environment was not considered homogeneous for yield in either location. Quantitative trait loci (QTLs) for the three characters were detected in linkage group (LG) 4. In relation to seed size, two QTLs were located in LG4 (QTL_SW1) and LG8 (QTL_SW2). QTL_SW1 accounted 20.3% of the total phenotypic variation and QTL_SW2 explained 10.1%. A QTL for yield (QTL_YD) was located in LG4 explaining around 13% of variation. QTL_YD might be pleiotropic with QTL_SW1. For days to flowering, a QTL (QTL_DF1) was located in LG4 for all environments analysed explaining around 20% of variation. QTL_DF1 was closely linked to QTL_SW1 and QTL_YD in LG4.     

Map-based analysis of the tenacious glume gene Tg-B1 of wild emmer and its role in wheat domestication

The domestication of wheat was instrumental in spawning the civilization of humankind, and it occurred through genetic mutations that gave rise to types with non-fragile rachises, soft glumes, and free-threshing seed. Wild emmer (Triticum turgidum ssp. dicoccoides), the tetraploid AB-genome progenitor of domesticated wheat has genes that confer tenacious glumes (Tg) that underwent genetic mutations to give rise to free-threshing wheat. Here, we evaluated disomic substitution lines involving chromosomes 2A and 2B of wild emmer accessions substituted for homologous chromosomes in tetraploid and hexaploid backgrounds. The results suggested that both chromosomes 2A and 2B of wild emmer possess genes that inhibit threshability. A population of recombinant inbred lines derived from the tetraploid durum wheat variety Langdon crossed with a Langdon — T. turgidum ssp. dicoccoides accession PI 481521 chromosome 2B disomic substitution line was used to develop a genetic linkage map of 2B, evaluate the genetics of threshability, and map the gene derived from PI 481521 that inhibited threshability. A 2BS linkage map comprised of 58 markers was developed, and markers delineated the gene to a 2.3 cM interval. Comparative analysis with maps containing the tenacious glume gene Tg-D1 on chromosome arm 2DS from Aegilops tauschii, the D genome progenitor of hexaploid wheat, revealed that the gene inhibiting threshability in wild emmer was homoeologous to Tg-D1 and therefore designated Tg-B1. Comparative analysis with rice and Brachypodium distachyon indicated a high level of divergence and poorly conserved colinearity, particularly near the Tg-B1 locus. These results provide a foundation for further studies involving Tg-B1, which, together with Tg-D1, had profound influences on wheat domestication.     

Improvements in the production of doubled haploids in durum wheat (<Emphasis Type="Italic">Triticum turgidum</Emphasis> L<Emphasis Type="Italic">.</Emphasis>) through isolated microspore culture

The objective of this study was to produce durum wheat doubled haploid (DH) plants through the induction of microspore embryogenesis. The microspore culture technique was improved to maximize production of green plants per spike using three commercial cultivars. Studies on factors such as induction media composition, induction media support and the stage and growth of donor plants were carried out in order to develop an efficient protocol to regenerate green and fertile DH plants. Microspores were plated on a C₁₇ induction culture medium with ovary co-culture and a supplement of glutathione plus glutamine; 300 g/l Ficoll Type-400 was incorporated to the induction medium support. Donor plants were fertilized with a combination of macro and microelements. With the cultivars ‘Ciccio’ and ‘Claudio’ an average of 36.5 and 148.5 fertile plants were produced, respectively, from 1,000 anthers inoculated. This technique was then used to produce fertile DH plants of potential agronomic interest from a collection of ten F₁ crosses involving cultivars of high breeding value. From these crosses 849 green plants were obtained and seed was harvested from 702 plants indicating that 83% of green plants were fertile and therefore were spontaneously DHs. No aneuploid plant was obtained. The 702 plants yielded enough seeds to be field tested. One of the DH lines obtained by microspore embryogenesis, named ‘Lanuza’, has been sent to the Spanish Plant Variety Office for Registration by the Batlle Seed Company. This protocol can be used instead of the labor-intensive inter-generic crossing with maize as an economically feasible method to obtain DHs for most crosses involving the durum wheat cultivars grown in Spain.     

Dissection of Additive, Epistatic Effect and Q × E Interaction of Quantitative Trait Loci Influencing Stigma Exsertion Under Water Stress in Rice

Four flowering related traits, spikelet number per panicle (SNP), percentage of single exserted stigma (PSES), dual exserted stigma (PDES) and total exserted stigma (PES) of a RI population with 185 lines under water stress and non-stress conditions for 2 years, were investigated in a drought tolerance screening facility. ANOVA results showed high significance between years, lines, and water stress treatments, together with interactions among them in pairs. Highest phenotypic correlation was found between PSES and PES (r = 0.9752^***), followed by PDES and PES (r = 0.7150^***), and PSES and PDES (r = 0.5424^***). Based on a linkage map of 203 SSR markers, six main effect QTLs were detected for SNP and three or four main effect QTLs were associated with PSES, PDES and PES under stress or non-stress conditions. There were one to nine pairs of epistatic QTLs influencing SNP and stigma exsertion. The contribution rates of additive and epistatic effects seemed to be in a low magnitude for most cases (0.76%-9.92%) while a few QTLs or QTL pairs explained more than 10% of total variance. Some main effect QTL and epistasis were commonly detected among PSES, PDES and PES, explaining the high positive correlation between them. Few QTLs were detected under both water stress and non-stress condition, implying that drought had severe impact on the genetic behaviors of both spikelet number and stigma exsertion.