Genomic selection for spot blotch in bread wheat breeding panels, full-sibs and half-sibs and index-based selection for spot blotch, heading and plant height.

KEY MESSAGE: Genomic selection is a promising tool to select for spot blotch resistance and index-based selection can simultaneously select for spot blotch resistance, heading and plant height. A major biotic stress challenging bread wheat production in regions characterized by humid and warm weather is spot blotch caused by the fungus Bipolaris sorokiniana. Since genomic selection (GS) is a promising selection tool, we evaluated its potential for spot blotch in seven breeding panels comprising 6736 advanced lines from the International Maize and Wheat Improvement Center. Our results indicated moderately high mean genomic prediction accuracies of 0.53 and 0.40 within and across breeding panels, respectively which were on average 177.6% and 60.4% higher than the mean accuracies from fixed effects models using selected spot blotch loci. Genomic prediction was also evaluated in full-sibs and half-sibs panels and sibs were predicted with the highest mean accuracy (0.63) from a composite training population with random full-sibs and half-sibs. The mean accuracies when full-sibs were predicted from other full-sibs within families and when full-sibs panels were predicted from other half-sibs panels were 0.47 and 0.44, respectively. Comparison of GS with phenotypic selection (PS) of the top 10% of resistant lines suggested that GS could be an ideal tool to discard susceptible lines, as greater than 90% of the susceptible lines discarded by PS were also discarded by GS. We have also reported the evaluation of selection indices to simultaneously select non-late and non-tall genotypes with low spot blotch phenotypic values and genomic-estimated breeding values. Overall, this study demonstrates the potential of integrating GS and index-based selection for improving spot blotch resistance in bread wheat.

Genetic dissection for head blast resistance in wheat using two mapping populations.

Wheat head blast is a dangerous fungal disease in South America and has recently spread to Bangladesh and Zambia, threatening wheat production in those regions. Host resistance as an economical and environment-friendly management strategy has been heavily relied on, and understanding the resistance loci in the wheat genome is very helpful to resistance breeding. In the current study, two recombinant inbred line (RIL) populations, Alondra/Milan (with 296 RILs) and Caninde#2/Milan-S (with 254 RILs and Milan-S being a susceptible variant of Milan), were used for mapping QTL associated with head blast resistance in field experiments. Phenotyping was conducted in Quirusillas and Okinawa, Bolivia, and in Jashore, Bangladesh, during the 2017-18 and 2018-19 cropping cycles. The DArTseq® technology was employed to genotype the lines, along with four STS markers in the 2NS region. A QTL with consistent major effects was mapped on the 2NS/2AS translocation region in both populations, explaining phenotypic variation from 16.7 to 79.4% across experiments. Additional QTL were detected on chromosomes 2DL, 7AL, and 7DS in the Alondra/Milan population, and 2BS, 4AL, 5AS, 5DL, 7AS, and 7AL in the Caninde#2/Milan-S population, all showing phenotypic effects <10%. The results corroborated the important role of the 2NS/2AS translocation on WB resistance and identified a few novel QTL for possible deployment in wheat breeding. The low phenotypic effects of the non-2NS QTL warrantee further investigation for novel QTL with higher and more stable effects against WB, to alleviate the heavy reliance on 2NS-based resistance.

QTL mapping for field resistance to wheat blast in the Caninde#1/Alondra population.

KEY MESSAGE: Wheat blast resistance in Caninde#1 is controlled by a major QTL on 2NS/2AS translocation and multiple minor QTL in an additive mode. Wheat blast (WB) is a devastating disease in South America, and it recently also emerged in Bangladesh. Host resistance to WB has relied heavily on the 2NS/2AS translocation, but the responsible QTL has not been mapped and its phenotypic effects in different environments have not been reported. In the current study, a recombinant inbred line population with 298 progenies was generated, with the female and male parents being Caninde#1 (with 2NS) and Alondra (without 2NS), respectively. Phenotyping was carried out in two locations in Bolivia, namely Quirusillas and Okinawa, and one location in Bangladesh, Jashore, with two sowing dates in each of the two cropping seasons in each location, during the years 2017-2019. Genotyping was performed with the DArTseq® technology along with five previously reported STS markers in the 2NS region. QTL mapping identified a major and consistent QTL on 2NS/2AS region, explaining between 22.4 and 50.1% of the phenotypic variation in different environments. Additional QTL were detected on chromosomes 1AS, 2BL, 3AL, 4BS, 4DL and 7BS, all additive to the 2NS QTL and showing phenotypic effects less than 10%. Two codominant STS markers, WGGB156 and WGGB159, were linked proximally to the 2NS/2AS QTL with a genetic distance of 0.9 cM, being potentially useful in marker-assisted selection.

Identification of Genomic Regions and Sources for Wheat Blast Resistance through GWAS in Indian Wheat Genotypes.

Wheat blast (WB) is a devastating fungal disease that has recently spread to Bangladesh and poses a threat to the wheat production in India, which is the second-largest wheat producing country in the world. In this study, 350 Indian wheat genotypes were evaluated for WB resistance in 12 field experiments in three different locations, namely Jashore in Bangladesh and Quirusillas and Okinawa in Bolivia. Single nucleotide polymorphisms (SNPs) across the genome were obtained using DArTseq® technology, and 7554 filtered SNP markers were selected for a genome-wide association study (GWAS). All the three GWAS approaches used identified the 2NS translocation as the only major source of resistance, explaining up to 32% of the phenotypic variation. Additional marker-trait associations were located on chromosomes 2B, 3B, 4D, 5A and 7A, and the combined effect of three SNPs (2B_180938790, 7A_752501634 and 5A_618682953) showed better resistance, indicating their additive effects on WB resistance. Among the 298 bread wheat genotypes, 89 (29.9%) carried the 2NS translocation, the majority of which (60 genotypes) were CIMMYT introductions, and 29 were from India. The 2NS carriers with a grand mean WB index of 6.6 showed higher blast resistance compared to the non-2NS genotypes with a mean index of 46.5. Of the 52 durum wheats, only one genotype, HI 8819, had the 2NS translocation and was the most resistant, with a grand mean WB index of 0.93. Our study suggests that the 2NS translocation is the only major resistance source in the Indian wheat panel analysed and emphasizes the urgent need to identify novel non-2NS resistance sources and genomic regions.

Wheat Blast: A Disease Spreading by Intercontinental Jumps and Its Management Strategies.

Wheat blast (WB) caused by Magnaporthe oryzae pathotype Triticum (MoT) is an important fungal disease in tropical and subtropical wheat production regions. The disease was initially identified in Brazil in 1985, and it subsequently spread to some major wheat-producing areas of the country as well as several South American countries such as Bolivia, Paraguay, and Argentina. In recent years, WB has been introduced to Bangladesh and Zambia via international wheat trade, threatening wheat production in South Asia and Southern Africa with the possible further spreading in these two continents. Resistance source is mostly limited to 2NS carriers, which are being eroded by newly emerged MoT isolates, demonstrating an urgent need for identification and utilization of non-2NS resistance sources. Fungicides are also being heavily relied on to manage WB that resulted in increasing fungal resistance, which should be addressed by utilization of new fungicides or rotating different fungicides. Additionally, quarantine measures, cultural practices, non-fungicidal chemical treatment, disease forecasting, biocontrol etc., are also effective components of integrated WB management, which could be used in combination with varietal resistance and fungicides to obtain reasonable management of this disease.

New Genotypes and Genomic Regions for Resistance to Wheat Blast in South Asian Germplasm.

Wheat blast (WB) disease, since its first identification in Bangladesh in 2016, is now an established serious threat to wheat production in South Asia. There is a need for sound knowledge about resistance sources and associated genomic regions to assist breeding programs. Hence, a panel of genotypes from India and Bangladesh was evaluated for wheat blast resistance and a genome-wide association study (GWAS) was performed. Disease evaluation was done during five crop seasons-at precision phenotyping platform (PPPs) for wheat blast disease at Jashore (2018-19), Quirusillas (2018-19 and 2019-20) and Okinawa (2019 and 2020). Single nucleotide polymorphisms (SNP) across the genome were obtained using DArTseq genotyping-by-sequencing platform, and in total 5713 filtered markers were used. GWAS revealed 40 significant markers associated with WB resistance, of which 33 (82.5%) were in the 2NS/2AS chromosome segment and one each on seven chromosomes (3B, 3D, 4A, 5A, 5D, 6A and 6B). The 2NS markers contributed significantly in most of the environments, explaining an average of 33.4% of the phenotypic variation. Overall, 22.4% of the germplasm carried 2NS/2AS segment. So far, 2NS translocation is the only effective WB resistance source being used in the breeding programs of South Asia. Nevertheless, the identification of non-2NS/2AS genomic regions for WB resistance provides a hope to broaden and diversify resistance for this disease in years to come.

Screening and Mapping for Head Blast Resistance in a Panel of CIMMYT and South Asian Bread Wheat Germplasm.

Wheat blast (WB) is a destructive disease in South America and its first outbreak in Bangladesh in 2016 posed a great risk to food security of South Asian countries. A genome wide association study (GWAS) was conducted on a diverse panel of 184 wheat genotypes from South Asia and CIMMYT. Phenotyping was conducted in eight field experiments in Bolivia and Bangladesh and a greenhouse experiment in the United States. Genotypic data included 11,401 SNP markers of the Illumina Infinium 15K BeadChip and four additional STS markers on the 2NS/2AS translocation region. Accessions with stable WB resistance across experiments were identified, which were all 2NS carriers. Nevertheless, a dozen moderately resistant 2AS lines were identified, exhibiting big variation among experiments. Significant marker-trait associations (MTA) were detected on chromosomes 1BS, 2AS, 6BS, and 7BL; but only MTAs on 2AS at the 2NS/2AS translocation region were consistently significant across experiments. The resistant accessions identified in this study could be used in production in South Asian countries as a preemptive strategy to prevent WB outbreak.

Identification of QTLs for Spot Blotch Resistance in Two Bi-Parental Mapping Populations of Wheat.

Spot blotch (SB) disease caused by the hemibiotrophic pathogen Bipolaris sorokiniana inflicting major losses to the wheat grown in warm and highly humid areas of the Indian subcontinent, including Bangladesh, necessitates identification of QTLs stably expressing in Indian subcontinent conditions. Thus, two RIL mapping populations, i.e., WC (WUYA × CIANO T79) and KC (KATH × CIANO T79), were phenotyped at Dinajpur, Bangladesh for three consecutive years (2013-2015) and genotyped on a DArTseq genotyping by sequencing (GBS) platform at CIMMYT, Mexico. In both populations, quantitative inheritance along with transgressive segregation for SB resistance was identified. The identified QTLs were mostly minor and were detected on 10 chromosomes, i.e., 1A, 1B, 2A, 2B, 2D, 4B, 4D, 5A, 5D, and 7B. The phenotypic variation explained by the identified QTLs ranged from 2.3-15.0%, whereby QTLs on 4B (13.7%) and 5D (15.0%) were the largest in effect. The identified QTLs upon stacking showed an additive effect in lowering the SB score in both populations. The probable presence of newly identified Sb4 and durable resistance gene Lr46 in the identified QTL regions indicates the importance of these genes in breeding for SB resistance in Bangladesh and the whole of South Asia.

Genome-wide association mapping for wheat blast resistance in CIMMYT's international screening nurseries evaluated in Bolivia and Bangladesh.

Wheat blast caused by the fungus Magnaporthe oryzae pathotype Triticum (MoT) is an emerging threat to wheat production. To identify genomic regions associated with blast resistance against MoT isolates in Bolivia and Bangladesh, we performed a large genome-wide association mapping study using 8607 observations on 1106 lines from the International Maize and Wheat Improvement Centre's International Bread Wheat Screening Nurseries (IBWSNs) and Semi-Arid Wheat Screening Nurseries (SAWSNs). We identified 36 significant markers on chromosomes 2AS, 3BL, 4AL and 7BL with consistent effects across panels or site-years, including 20 markers that were significant in all the 49 datasets and tagged the 2NS translocation from Aegilops ventricosa. The mean blast index of lines with and without the 2NS translocation was 2.7 ± 4.5 and 53.3 ± 15.9, respectively, that substantiates its strong effect on blast resistance. Furthermore, we fingerprinted a large panel of 4143 lines for the 2NS translocation that provided excellent insights into its frequency over years and indicated its presence in 94.1 and 93.7% of lines in the 2019 IBWSN and SAWSN, respectively. Overall, this study reinforces the effectiveness of the 2NS translocation for blast resistance and emphasizes the urgent need to identify novel non-2NS sources of blast resistance.