Phenomic selection: a low-cost and high-throughput method based on indirect predictions. Proof of concept on wheat and poplar

Renaud Rincent, Jean-Paul Charpentier, Patricia Faivre-Rampant, Etienne Paux, Jacques Le Gouis, Catherine Bastien, Vincent Segura

G3-Genes-Genomes-Genetics (2018)

Abstract Genomic selection – the prediction of breeding values using DNA polymorphisms – is a disruptive method that has widely been adopted by animal and plant breeders to increase productivity. It was recently shown that other sources of molecular variations such as those resulting from transcripts or metabolites could be used to accurately predict complex traits. These endophenotypes have the advantage of capturing the expressed genotypes and consequently the complex regulatory networks that occur in the different layers between the genome and the phenotype. However, obtaining such omics data at very large scales, such as those typically experienced in breeding, remains challenging. As an alternative, we proposed using near-infrared spectroscopy (NIRS) as a high-throughput, low cost and non-destructive tool to indirectly capture endophenotypic variants and compute relationship matrices for predicting complex traits and coined this new approach “phenomic selection” (PS). We tested PS on two species of economic interest (Triticum aestivum L. and Populus nigra L.) using NIRS on various tissues (grains, leaves, wood). We showed that one could reach predictions as accurate as with molecular markers, for developmental, tolerance and productivity traits, even in environments radically different from the one in which NIRS were collected. Our work constitutes a proof of concept and provides new perspectives for the breeding community, as PS is theoretically applicable to any organism at low cost and does not require any molecular information.

Key periods and effects of meteorological factors affecting incidence of wheat black point in the Yellow and Huai wheat area of China

Qiao-Yun Li , Si-Yu Wang , Shou-Wei Chang , Kai-Ge Xu , Meng-Yu Li , Qiao-Qiao Xu , Yu-Mei Jiang , Ji-Shan Niu

Crop Protection (2019)

Abstract To determine the key periods and effects of meteorological factors affecting the incidence of black point, the correlations between 14 meteorological variables and incidence of black point were analyzed using 23 susceptible
wheat genotypes planted at three locations in two years in the Yellow and Huai Wheat Area of China. The results showed that the incidence of black point and meteorological factors varied considerably across locations and years. There was a significantly negative correlation between temperature-related variables (daily average temperature, days with temperature > 30 C, etc.) and black point incidence at 26–40 days after heading. Humidity-related variables (daily relative humidity, rainfall days, etc.) except precipitation were positively correlated with black point incidence at 1–20 days after heading. When the daily average temperature decreased by 1 C at 31–35 days after heading, the incidence of black point increased by approximately 5.5%, and when the daily relative humidity increased by 10% at 11–15 days after heading, the incidence increased by approximately 9.4%. There was a significant negative correlation between daily sunshine duration and black point incidence at 1–15 days and 26–40 days after heading. In conclusion, the key periods and meteorological factors affecting black point incidence are a humid environment at 1–15 days, lower temperature at 26–40 days, and a short period of sunshine after heading. These results provide important information for the control of black point in wheat.

Screening bread wheat germplasm for resistance to take-all disease (Gaeumannomyces graminis var. tritici) in greenhouse conditions

M. Gholizadeh Vazvani, H. Dashti, R. Saberi Riseh, and M. R. Bihamta

J. Agr. Sci. Tech. (2017)

Abstract Root and crown rot of wheat is caused by the fungus Gaeumannomyces graminis var. tritici. « Take-all » is an important disease affecting wheat, and its incidence has been reported in several provinces of Iran. To identify resistant cultivars, bread wheat germplasm should be evaluated. To evaluate bread wheat germplasm in response to Iranian isolate fungus (T-41) of Gaeumannomyces graminis var. tritici, 333 genotype of bread wheat, collected from different locations of Iran and other countries were evaluated to take-all in greenhouse conditions. Two experiments were conducted, the first with 89 and the second with 244 genotypes. The measured traits were amount of root and crown infection, disease intensity, wet and dry biomass, and height of shoots. Analysis of variance and means comparison for the parameters indicated that in the first experiment, two genotypes were resistant to the disease, and the rates of disease intensity in these genotypes were 0.13 and 0.06. In the second experiment, five completely resistant genotypes were identified with disease intensity ratings of ‘0’. The identified resistant genotypes screened from both experiments were re-evaluated, and the results were the same. Mean comparison between winter and spring types for dry weight and disease intensity showed that winter wheat is more resistant than spring type. The results of this research showed that there is resistance resource to take-all (T-41 isolate), in this germplasm.Since the experiment was conducted in greenhouse conditions, these genotypes should be tested against this disease in infected conditions at field.

Identification and mapping of two adult plant leaf rust resistance genes in durum wheat

Caixia Lan, Zhikang Li, Sybil A. Herrera-Foessel, Julio Huerta-Espino, Bhoja R. Basnet, Susanne Dreisigacker, Yong Ren, Evans Lagudah, Ravi P. Singh

Molecular Breeding, 2019

Abstract The International Maize and Wheat Improvement Center (CIMMYT)-derived durum wheat line Quetru is moderately resistant to leaf rust and displays disease severities of 15–30% at the adult plant stage. Atil C2000 is moderately susceptible to leaf rust at adult plant stage and displays severities of 20–60%. These two durum wheats were crossed with the susceptible line Atred#1, and the respective recombinant inbred line populations were phenotyped for resistance to leaf rust in field trials in four environments in Mexico. The phenotypic segregation in the Atred#1 × Atil C2000 population was attributed to the pleiotropic adult plant resistance (APR) gene Lr46 based on the closest marker cslv46G22 located within 1.4 cM. Lr46 reduced leaf rust severity by 19.6–35.5%, and it was also identified in the Atred#1 × Quetru population, where it reduced leaf rust severity by 28.5–57.7% depending on the environment. We also identified a putatively novel, race-specific APR gene LrQ in Quetru that is located on the Chromosome 6BL and flanked by SNP markers AX-95144243 and AX-95155193. These two markers have been converted into kompetitive allele–specific PCR (KASP) markers and validated in the population. LrQ was ineffective at the seedling stage but reduced leaf rust severity by 37.3% on average over four field trials. The combination of LrQ and Lr46 resulted in significantly reduced leaf rust severity in the field and could be used to breed improved durum wheat varieties.

Characterization and mapping of leaf rust resistance in four durum wheat cultivars

Dhouha Kthiri, Alexander Loladze, P. R. MacLachlan, Amidou N’Diaye, Sean Walkowiak, Kirby Nilsen, Susanne Dreisigacker, Karim Ammar, Curtis J. Pozniak.

Plos One, 2018

Abstract Widening the genetic basis of leaf rust resistance is a primary objective of the global durum wheat breeding effort at the International Wheat and Maize Improvement Center (CIMMYT). Breeding programs in North America are following suit, especially after the emergence of new races of Puccinia triticina such as BBG/BP and BBBQD in Mexico and the United States, respectively. This study was conducted to characterize and map previously unde- scribed genes for leaf rust resistance in durum wheat and to develop reliable molecular markers for marker-assisted breeding. Four recombinant inbred line (RIL) mapping popula- tions derived from the resistance sources Amria, Byblos, Geromtel_3 and Tunsyr_2, which were crossed to the susceptible line ATRED #2, were evaluated for their reaction to the Mexican race BBG/BP of P. triticina. Genetic analyses of host reactions indicated that leaf rust resistance in these genotypes was based on major seedling resistance genes. Allelism tests among resistant parents supported that Amria and Byblos carried allelic or closely linked genes. The resistance in Geromtel_3 and Tunsyr_2 also appeared to be allelic. Bulked segregant analysis using the Infinium iSelect 90K single nucleotide polymorphism (SNP) array identified two genomic regions for leaf rust resistance; one on chromosome 6BS for Geromtel_3 and Tunsyr_2 and the other on chromosome 7BL for Amria and Byblos. Polymorphic SNPs identified within these regions were converted to kompetitive allele-spe- cific PCR (KASP) assays and used to genotype the RIL populations. KASP markers usw215and usw218were the closest to the resistance genes in Geromtel_3 and Tunsyr_2, while usw260was closely linked to the resistance genes in Amria and Byblos. DNA sequences associated with these SNP markers were anchored to the wild emmer wheat (WEW) reference sequence, which identified several candidate resistance genes. The molecular markers reported herein will be useful to effectively pyramid these resistance genes with other previously marked genes into adapted, elite durum wheat genotypes.

Development and validation of molecular markers for grain cadmium in durum wheat

Salsman Evan, Kumar Ajay, Abuhammad Wesam, Abbasabadi Atena Oladzad, Dobrydina Marina, Chao Shiaoman, Li Xuehui, Manthey Frank A, Elias Elias M.

Molecular Breeding, 2018

Abstract Durum wheat is capable of accumulating cadmium, a toxic heavy metal, in the grain at levels that have been deemed unsafe for human consumption. Pre- vious studies have identified genetic variation as well as markers associated with Cd accumulation in durum wheat, which can be exploited to develop low Cd culti- vars. Because the phenotyping for Cd content is very expensive, KASP markers were developed from molec- ular markers associated with grain Cd and tested for their usefulness for marker-assisted breeding. A total of 1278 unique genotypes from preliminary and ad- vanced yield trials grown at multiple locations for 2 years were evaluated for grain Cd as well as screened for markers associated with Cd uptake. One marker on chromosome 5B was polymorphic in all crosses be- tween high and low Cd parents and had r2 values ranging from 0.38 to 0.85. Two other markers on the same chromosome predicted similar levels of variation in many trials; however, they were not polymorphic in all populations. The KASP markers accurately predicted up to 97% of the lines for Cd phenotype in different trials. This study identified two markers, Cad-5B and Ex_c1343_2570756, with an average prediction accu- racy of 84–88%. These markers could be useful for marker-assisted selection for low grain Cd in durum wheat.

Simultaneous improvement of grain yield and protein content in durum wheat by different phenotypic indices and genomic selection

Rapp M., Lein V., Lacoudre F., Lafferty J., Müller E., Vida G., Bozhanova V., Ibraliu A., Thorwarth P., Piepho H. P., Leiser W. L., Würschum T., Longin C. F. H.

Theoretical and Applied Genetics, 2018

Abstract Grain yield and protein content are of major importance in durum wheat breeding, but their negative correlation has hampered their simultaneous improvement. To account for this in wheat breeding, the grain protein deviation (GPD) and the protein yield were proposed as targets for selection. The aim of this work was to investigate the potential of different indices to simultaneously improve grain yield and protein content in durum wheat and to evaluate their genetic architecture towards genomics-assisted breeding. To this end, we investigated two different durum wheat panels comprising 159 and 189 genotypes, which were tested in multiple field locations across Europe and genotyped by a genotyping-by-sequencing approach. The phenotypic analyses revealed significant genetic variances for all traits and heritabilities of the phenotypic indices that were in a similar range as those of grain yield and protein content. The GPD showed a high and positive correla- tion with protein content, whereas protein yield was highly and positively correlated with grain yield. Thus, selecting for a high GPD would mainly increase the protein content whereas a selection based on protein yield would mainly improve grain yield, but a combination of both indices allows to balance this selection. The genome-wide association mapping revealed a complex genetic architecture for all traits with most QTL having small effects and being detected only in one germplasm set, thus limiting the potential of marker-assisted selection for trait improvement. By contrast, genome-wide prediction appeared promising but its performance strongly depends on the relatedness between training and prediction sets.

Genome-Wide Association and Prediction of Grain and Semolina Quality Traits in Durum Wheat Breeding Populations

Fiedler Jason D., Salsman Evan, Liu Yuan, Michalak de Jiménez Monika, Hegstad Justin B., Chen Bingcan, Manthey Frank A., Chao Shiaoman, Xu Steven, Elias Elias M., Li Xuehui

The Plant Genome, 2017

Abstract Grain yield and semolina quality traits are essential selection criteria in durum wheat breeding. However, high phenotypic screening costs limit selection to relatively few breeding lines in late generations. This selection paradigm confers relatively low selection efficiency due to the advancement of undesirable lines into expensive yield trials for grain yield and quality trait testing. Marker-aided selection can enhance selection efficiency, especially for traits that are difficult or costly to phenotype. The aim of this study was to identify major quality trait quantitative trait loci (QTL) for marker-assisted selection (MAS) and to explore potential application of genomic selection (GS) in a durum wheat breeding program. In this study, genome-wide association mapping was conducted for five quality traits using 1184 lines from the North Dakota State University (NDSU) durum wheat breeding program. Several QTL associated with test weight, semolina color, and gluten strength were identified. Genomic selection models were developed and forward prediction accuracies of 0.27 to 0.66 were obtained for the five quality traits. Our results show the potential for grain and semolina quality traits to be selected more efficiently through MAS and GS with further refinement. Considerable opportunity exists to extend these techniques to other traits such as grain yield and agronomic characteristics, further improving breeding efficiency in durum cultivar development.

Epistatic determinism of durum wheat resistance to the Wheat Spindle Streak Mosaic Virus

Holtz Yan, Bonnefoy Michel, Viader Véronique, Ardisson Morgane, Rode Nicolas O., Poux Gérard, Roumet Pierre, Marie-Jeanne Véronique, Ranwez Vincent, Santoni Sylvain, Gouache David, David Jacques

Theoretical ans Applied Genetics, 2017

Abstract Wheat spindle streak mosaic virus (WSSMV) is a major disease of durum wheat in Europe and North America. Breeding WSSMV-resistant cultivars is cur- rently the only way to control the virus since no treatment is available. This paper reports studies of the inheritance of WSSMV resistance using two related durum wheat populations obtained by crossing two elite cultivars with a WSSMV-resistant emmer cultivar. In 2012 and 2015, 354 recombinant inbred lines (RIL) were phenotyped using vis- ual notations, ELISA and qPCR and genotyped using locus targeted capture and sequencing. This allowed us to build a consensus genetic map of 8568 markers and identify three chromosomal regions involved in WSSMV resistance. Two major regions (located on chromosomes 7A and 7B) jointly explain, on the basis of epistatic interactions, up to 43% of the phenotypic variation. Flanking sequences of our genetic markers are provided to facilitate future marker-assisted selection of WSSMV-resistant cultivars.

Breeding strategies and advances in line selection for Fusarium head blight resistance in wheat

Steiner Barbara, Buerstmayr Maria, Michel Sebastian, Schweiger Wolfgang, Lemmens Marc, Buerstmayr Hermann

Tropical Plant Pathology, 2017

Abstract Fusarium head blight (FHB) is a fungal disease of worldwide importance to small grain cereals that may lead to severe losses in both yield and quality. The development of resistant varieties is the most effective approach for managing the disease. Genetic variation for FHB resistance is large, in- cluding ‘exotic’ and ‘native’ wheat germplasm. Methods for selecting improved lines include: 1) phenotypic selection with direct symptom evaluation; 2) marker-assisted selection for well-characterized QTL and 3) genomic selection employing genome-wide prediction models. Breeding programs need to find the optimal deployment of the complementary ap- proaches according to their available facilities, resources and requirements. This review aims to summarize recent advances in FHB resistance breeding, thereby discussing the impor- tance ofmorphological traits like the extent ofretained anthers after flowering, its suitability for indirect selection and the pronounced association of the semi-dwarfing allele Rht-D1b with increased anther retention and FHB severity. Marker- assisted selection is successfully applied to select for large- effect QTL, especially for the most prominent resistance QTL Fhb1 in bread wheat, as well as in durum wheat as recently demonstrated. The resistance locus Fhb1 has been partly elucidated, a pore-forming toxin-like gene confers re- sistance against fungal spread. Genomic selection for FHB resistance appears promising especially for breeding programs deploying ‘native’ resistance sources with many small-effect QTL.

Single Marker and Haplotype-Based Association Analysis of Semolina and Pasta Colour in Elite Durum Wheat Breeding Lines Using a High-Density Consensus Map

N’Diaye Amidou, Haile Jemanesh K., Cory Aron T., Clarke Fran R., Clarke John M., Knox Ron E., Pozniak Curtis J.

Plos One, 2017

Abstract  Association mapping is usually performed by testing the correlation between a single marker and phenotypes. However, because patterns of variation within genomes are inherited as blocks, clustering markers into haplotypes for genome-wide scans could be a worthwhile approach to improve statistical power to detect associations. The availability of high-density molecular data allows the possibility to assess the potential of both approaches to identify marker-trait associations in durum wheat. In the present study, we used single marker- and haplotype-based approaches to identify loci associated with semolina and pasta colour in durum wheat, the main objective being to evaluate the potential benefits of haplotype-based analysis for identifying quantitative trait loci. One hundred sixty-nine durum lines were geno- typed using the Illumina 90K Infinium iSelect assay, and 12,234 polymorphic single nucleo- tide polymorphism (SNP) markers were generated and used to assess the population structure and the linkage disequilibrium (LD) patterns. A total of 8,581 SNPs previously localized to a high-density consensus map were clustered into 406 haplotype blocks based on the average LD distance of 5.3 cM. Combining multiple SNPs into haplotype blocks increased the average polymorphism information content (PIC) from 0.27 per SNP to 0.50 per haplotype. The haplotype-based analysis identified 12 loci associated with grain pig- ment colour traits, including the five loci identified by the single marker-based analysis. Fur- thermore, the haplotype-based analysis resulted in an increase of the phenotypic variance explained (50.4% on average) and the allelic effect (33.7% on average) when compared to single marker analysis. The presence of multiple allelic combinations within each haplotype locus offers potential for screening the most favorable haplotype series and may facilitate marker-assisted selection of grain pigment colour in durum wheat. These results suggest a benefit of haplotype-based analysis over single marker analysis to detect loci associated with colour traits in durum wheat.