QTL mapping of seedling and field resistance to stem rust in DAKIYE/Reichenbachii durum wheat population

Stem rust caused by the fungus Puccinia graminis f.sp. tritici Eriks. & E. Henn. (Pgt) threatens the global production of both durum wheat (Triticum turgidum L. ssp. durum (Desf.) Husnot) and common wheat (Triticum aestivum L.). The objective of this study was to evaluate a durum wheat recombinant inbred line (RIL) population from a cross between a susceptible parent ‘DAKIYE’ and a resistant parent ‘Reichenbachii’ developed by the International Center for the Improvement of Maize and Wheat (CIMMYT) 1) for seedling response to races JRCQC and TTRTF and 2) for field response to a bulk of the current Pgt races prevalent in Ethiopia and Kenya and 3) to map loci associated with seedling and field resistances in this population. A total of 224 RILs along with their parents were evaluated at the seedling stage in the Ethiopian Institute for Agricultural Research greenhouse at Debre Zeit, Ethiopia and in the EIAR and KALRO fields in Ethiopia and Kenya, for two seasons from 2019 to 2020. The lines were genotyped using the genotyping-by-sequencing approach. A total of 843 single nucleotide polymorphism markers for 175 lines were used for quantitative trait locus (QTL) analyses. Composite interval mapping (CIM) identified three QTL on chromosomes 3B, 4B and 7B contributed by the resistant parent. The QTL on chromosome 3B was identified at all growth stages and it explained 11.8%, 6.5%, 6.4% and 15.3% of the phenotypic variation for responses to races JRCQC, TTRTF and in the field trials ETMS19 and KNMS19, respectively. The power to identify additional QTL in this population was limited by the number of high-quality markers, since several markers with segregation distortion were eliminated. A cytological study is needed to understand the presence of chromosomal rearrangements. Future evaluations of additional durum lines and RIL families identification of durable adult plant resistance sources is crucial for breeding stem rust resistance in durum wheat in the future

QTL MAPPING OF STEM RUST RESISTANCE LOCI IN DURUM WHEAT POPULATIONS

256 pagesStem rust caused by Puccinia graminis f. sp. tritici Eriks. & Henn is the most destructive disease of durum and common wheat. The main focus of this study is to identify loci associated with stem rust resistance in durum wheat using association mapping and linkage mapping. A panel of 283 lines and 224 recombinant inbred lines (RILs) from a cross between ‘Reichenbachii’ and ‘DAKIYE’ developed by the durum wheat breeding program of the International Maize and Wheat Improvement Center (CIMMYT) were used for the study. The panel was evaluated against races TTKSK, TKTTF, JRCQC and TTRTF at the seedling stage and TKTTF and JRCQC in the field in Ethiopia from 2018 to 2019 for two seasons. The same panel was evaluated against bulk of multiple stem rust races prevalent in Ethiopia and Kenya from 2018 to 2019 in five environments. Genome-wide association study (GWAS) was conducted using 26,439 single nucleotide polymorphism (SNP) markers for seedling response (280 lines) and field response (283 lines) to stem rust. The RILs along with the two parents were evaluated for response to bulk of multiple stem rust races in Ethiopia and Kenya for two seasons from 2019 to 2020. Linkage analyses were conducted using 843 SNP markers for 175 lines. For GWAS of seedling response, a mixed linear model (MLM) identified 17 quantitative trait loci (QTL) of which eight were putatively novel while FarmCPU identified 20 QTL and 12 were likely novel. For field resistance to races TKTTF and JRCQC, MLM detected 19 QTL of which 12 were likely novel while FarmCPU detected 16 QTL and seven were putatively novel. For resistance to multiple Pgt races in East Africa, 160 significant marker-trait associations (MTAs) grouped into 42 QTL were identified using MLM and FarmCPU and 21 QTL were likely novel. From previously reported Sr genes, the regions of Sr7a, Sr8a, Sr8155B1, Sr11, Sr12, alleles of Sr13, Sr17, Sr22/Sr25, and Sr49 were identified. For the biparental population, composite interval mapping (CIM) identified three QTL on chromosomes 3B (QSr.cnl-3B), 4B (QSr.cnl-4B) and 7B (QSr.cnl-7B). These three QTL contributed by the resistant parent explained 4.7% to 15.3% of the phenotypic variation and all match previously reported loci. Lines with multiple-race stem rust resistance can be used as parents in durum wheat resistance breeding to stem rust and markers identified in the GWAS can be used in marker-assisted selection (MAS) once validated in a different population. Further study on the validation of allele specific markers and allelism tests in the Sr13 region of chromosome 6A is needed. Future evaluation of large numbers of durum wheat lines and searching for durable adult plant resistance gene is crucial in resistance breeding of durum wheat

Influence of seed rate and row spacing on seed multiplication factor and yield of durum wheat in Ethiopia

Abstract Optimum seeding rate and row spacing are important for uniform crop establishment and harvest of quality seed. Field experiment was conducted at three locations in 2014 and 2015 to study the influence of seed rate and row spacing on seed multiplication factor and yield of durum wheat. Triplicate split plot design was used. The highest seed yield was found at a seed rate of 125 kg ha−1 with a row spacing of 10 cm in 2014 but not significant with the seed rates of 100 kg ha−1 at 10 cm spacing, 75 kg ha−1 at 20 cm row spacing in 2014, and 150 kg ha−1 at 10 cm row spacing in 2015 at Debre Zeit. At Chefe Donsa, the highest seed yield (4.75 ton) was harvested at a seed rate of 100 kg ha−1. At Minjar, seed yield was not affected by seeding rate. Seed multiplication factor was higher at a seed rate of 50 kg ha−1 and spacing of 20 cm at Debre Zeit. At Chefe Donsa, the highest seed multiplication ratio (97.3) was observed in 2015 at a seed rate of 50 kg ha−1 with row spacing of 30 cm. Seed multiplication factor decreased with increasing seed rate at all testing locations. Sowing of 100 kg seeds per hectare with 20 cm spacing gave optimum seed yield over the testing locations. With limited seed availability of nucleus seed, 50 and 75 kg ha−1 with a spacing of 20 cm is appropriate to upsurge seed multiplication ratio

Effects of QTL on the response of RILs to races JRCQC and TTRTF, the A allele was from the susceptible parent (‘DAKIYE’) and the B allele was from the resistant parent (‘Reichenbachii’).

Effects of QTL on the response of RILs to races JRCQC and TTRTF, the A allele was from the susceptible parent (‘DAKIYE’) and the B allele was from the resistant parent (‘Reichenbachii’).</p

Distribution of CI of field responses of the RIL population derived from ‘Reichenbachii’ /DAKIYE cross in four testing environments.

Distribution of CI of field responses of the RIL population derived from ‘Reichenbachii’ /DAKIYE cross in four testing environments.</p

Effects of QTL on the response of RILs across the testing environments, the A allele was from the susceptible parent (‘DAKIYE’) and the B allele was from the resistant parent (‘Reichenbachii’).

Effects of QTL on the response of RILs across the testing environments, the A allele was from the susceptible parent (‘DAKIYE’) and the B allele was from the resistant parent (‘Reichenbachii’).</p

Genetic linkage map constructed from SNP markers derived from genotyping-by-sequencing in a recombinant inbred line population from a cross between Reichenbachii and DAKIYE.

Genetic linkage map constructed from SNP markers derived from genotyping-by-sequencing in a recombinant inbred line population from a cross between Reichenbachii and DAKIYE.</p

Summary of analysis of variance and QTL by environment interaction.

(DOCX)</p

Percentage of resistant, susceptible, and transgressive segregants of RILs evaluated for response to multiple stem rust races across four testing environments.

Percentage of resistant, susceptible, and transgressive segregants of RILs evaluated for response to multiple stem rust races across four testing environments.</p

Lists of marker genotypes with significant segregation distortion at Bonefferroni threshold.

(DOCX)</p