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Wheat Breeding, Genomic Selection, and Phenomics

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A special issue of Plants (ISSN 2223-7747). This special issue belongs to the section "Plant Genetics, Genomics and Biotechnology".

Deadline for manuscript submissions: closed (31 May 2022) | Viewed by 26483

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Special Issue Editors

Dr. Jemanesh Haile

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Guest Editor

Wheat Breeding and Genetics, Department of Plant Sciences/ Crop Development Centre, University of Saskatchewan, Saskatoon, SK S7N 5A8, Canada
Interests: pre-breeding and breeding of wheat for a higher yield; superior quality and resistance to FHB; leaf and stem rust; genomic selection for improving quantitative traits

Dr. Amidou N’Diaye

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Guest Editor

Wheat Breeding and Genetics, Department of Plant Sciences/ Crop Development Centre, University of Saskatchewan, Saskatoon, SK S7N 5A8, Canada
Interests: machine learning for sustainable agriculture; predictive modelling using multi-omics data; functional phenomics

Special Issue Information

Dear Colleagues,

Genomic selection (GS), first proposed by Meuwissen et al. in 2001, shows great promise to strongly increase the rate of genetic improvement in plant breeding programs. It allows for a comparative larger gain from selection by estimating all marker effects simultaneously, and the subsequent selection of genetically superior individuals is based on their genomic estimated breeding value (GEBV), instead of using a few significant markers as in classical marker assisted selection (MAS). In GS, a training population is genotyped with genome-wide markers and is phenotyped for the trait under selection. GS models are then trained with the marker and phenotype data, and the model is used to predict the breeding value of a new set of individuals (selection candidates) that have been genotyped, but have not been phenotyped. The prediction accuracies of GS depend on several factors, including the genetic architecture of the target traits, the number of traits considered at a given time, and the statistical models. GS is ideal for complex traits with a lower heritability and a complex genetic architecture. With this genetic architecture, whole-genome prediction models, as employed in GS, have consistently shown superior prediction accuracy over models that use significance testing to first identify individual markers, and then model the effect of these markers.

Genomic selection has been well established in the field of animal breeding, but many plant breeding programs worldwide are still evaluating the optimal strategy and stage for implementation in a breeding program. Wheat breeding programs typically require 10–15 years to transfer novel genes into elite germplasms. Through the application of GS, it is possible to select new parents purely based on GEBV, before being entered in field trials and nurseries. We expect GS to be intensively applied in wheat breeding programs, given its numerous advantages, such as improving selection gain, reducing the need for labor-intensive and costly phenotyping at disease nurseries, and accelerating the utilization of genetic variation. It is also possible to predict breeding values for a very large number of candidates that could not be feasibly evaluated phenotypically, thus leading to increased selection intensity. However, there is still limited information on the implementation of GS in applied wheat breeding programmes.

Therefore, this Special Issue of Plants is composed to address this question by focusing on empirical GS studies addressing important traits in wheat; combining GS with MAS; modelling multiple traits, epistatics, and genotypes through environmental interaction; enhancing the predictability of GS for wheat breeding through machine learning empowered high-throughput and precise phenotyping; and cost effective applications of “omics” data.

Dr. Jemanesh Haile
Dr. Amidou N’Diaye
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Plants is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

GS
GEBV
wheat
phenomics
genotype by envirnment interaction
machine learning
high-throughput phenotyping
“omics” data
genetic gain
selection intensity

Published Papers (8 papers)

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Research

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14 pages, 3208 KiB

Open AccessArticle

Path Coefficient and Principal Component Analyses for Biomass Allocation, Drought Tolerance and Carbon Sequestration Potential in Wheat

by Kwame W. Shamuyarira, Hussein Shimelis, Sandiswa Figlan and Vincent Chaplot

Plants 2022, 11(11), 1407; https://0-doi-org.brum.beds.ac.uk/10.3390/plants11111407 - 26 May 2022

Cited by 5 | Viewed by 1840

Abstract

Increased root biomass allocation could serve as a proxy trait for selecting crop ideotypes with drought tolerance and carbon sequestration potential in agricultural soils. The objective of this study was to assess the magnitude of the relationship between root biomass and yield components and to identify influential traits so as to optimise genotype selection for enhanced biomass allocation, drought tolerance and carbon sequestration potential in bread wheat (Triticum aestivum L.). One-hundred wheat genotypes consisting of 10 parents and 90 derived F₂ families were evaluated under drought-stressed and non-stressed conditions at two different sites. Data were collected for days to heading (DTH), days to maturity (DTM), plant height, productive tiller number (TN), spike length, spikelets per spike (SPS), kernels per spike (KPS), thousand kernel weight (TKW), shoot biomass, root biomass, total plant biomass (PB), root-to-shoot ratio (RS) and grain yield. There was significant (p < 0.05) genetic variation in most assessed traits, TN and RS being exceptions. Root biomass had significant positive correlations with grain yield under drought-stressed (r = 0.28) and non-stressed (r = 0.41) conditions, but a non-significant correlation was recorded for RS and grain yield. Notably, both root biomass and shoot biomass had significant positive correlations under both water regimes, revealing the potential of increasing both traits with minimal biomass trade-offs. The highest positive direct effects on grain yield were found for KPS and PB under both water regimes. The present study demonstrated that selection based on KPS and PB rather than RS will be more effective in ideotype selection of segregating populations for drought tolerance and carbon sequestration potential. Full article

(This article belongs to the Special Issue Wheat Breeding, Genomic Selection, and Phenomics)

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14 pages, 1922 KiB

Open AccessArticle

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

by Sahar Bennani, Ahmed Birouk, Mohammed Jlibene, Miguel Sanchez-Garcia, Nasserelhaq Nsarellah, Fatima Gaboun and Wuletaw Tadesse

Plants 2022, 11(7), 986; https://0-doi-org.brum.beds.ac.uk/10.3390/plants11070986 - 04 Apr 2022

Cited by 4 | Viewed by 2193

Abstract

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. Full article

(This article belongs to the Special Issue Wheat Breeding, Genomic Selection, and Phenomics)

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15 pages, 1084 KiB

Open AccessArticle

Evaluation of Wheat Resistance to Snow Mold Caused by Microdochium nivale (Fr) Samuels and I.C. Hallett under Abiotic Stress Influence in the Central Non-Black Earth Region of Russia

by Sulukhan K. Temirbekova, Ivan M. Kulikov, Mukhtar Z. Ashirbekov, Yuliya V. Afanasyeva, Olga O. Beloshapkina, Lev G. Tyryshkin, Evgeniy V. Zuev, Rima N. Kirakosyan, Alexey P. Glinushkin, Elena S. Potapova and Nazih Y. Rebouh

Plants 2022, 11(5), 699; https://0-doi-org.brum.beds.ac.uk/10.3390/plants11050699 - 04 Mar 2022

Cited by 10 | Viewed by 2484

Abstract

Microdochium nivale is one of the most harmful fungal diseases, causing colossal yield losses and deteriorating grain quality. Wheat genotypes from the world collection of the N.I. Vavilov Institute (VIR) were evaluated for fifty years to investigate their resistance to biotic stress factors (M. nivale). Between 350 to 1085 of winter wheat genotypes were investigated annually. Ten out of fifty years were identified as rot epiphytotics (1978, 1986, 1989, 1990, 1993, 1998, 2001, 2003, 2005 and 2021). The wheat collection was investigated by following the VIR methodological requirements and CMEA unified classification of Triticum aestivum L. The field investigations were carried out in the early spring during fixed-route observations and data collection was included on the spread and development degree of the disease, followed by microbiological and microscopic pathogen identifications. The observations revealed that the primary reason for pink snow mold to infect the wheat crops was abiotic stress factors, such as thawed soil covered in snow that increased the soil temperature by 1.0–4.6 °C above normal. Under these conditions, the plants kept growing, quickly exhausting their carbohydrate and protein resources, thus weakening their immune systems, which made them an easy target for different infections, mainly cryophilic fungi, predominantly Microdochium nivale in the Moscow region. In some years, the joint effect of abiotic and biotic stresses caused crop failure, warranting the replanting of the spring wheat. The investigated wheat genotypes exhibited variable resistance to pink snow mold. The genotypes Mironovskaya 808 (k-43920) from Ukraine;l Nemchinovskaya 846 (k-56861), from Russia; Novobanatka (k-51761) from Yugoslavia; Liwilla (k-57580) from Poland; Zdar (UH 7050) from the Czech Republic; Maris Plowman (k-57944) from the United Kingdom; Pokal (k-56827) from Austria; Hvede Sarah (k-56289) from Denmark; Moldova 83 (k-59750) from Romania; Compal (k-57585) from Germany; Linna (k-45889) from Finland and Kehra (k-34228) from Estonia determined the sources, stability and tolerance to be used in advanced breeding programs. Full article

(This article belongs to the Special Issue Wheat Breeding, Genomic Selection, and Phenomics)

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19 pages, 1349 KiB

Open AccessFeature PaperArticle

Hybrid Seed Set in Relation with Male Floral Traits, Estimation of Heterosis and Combining Abilities for Yield and Its Components in Wheat (Triticum aestivum L.)

by Samira El Hanafi, Souad Cherkaoui, Zakaria Kehel, Miguel Sanchez-Garcia, Jean-Benoit Sarazin, Stephen Baenziger and Wuletaw Tadesse

Plants 2022, 11(4), 508; https://0-doi-org.brum.beds.ac.uk/10.3390/plants11040508 - 14 Feb 2022

Cited by 8 | Viewed by 2573

Abstract

Breeding hybrids with maximum heterosis requires efficient cross-pollination and an improved male sterility system. Renewed efforts have been made to dissect the phenotypic variation and genetic basis of hybrid floral traits, although the potential of tailoring the appropriate flower design on seed setting is less known. To this end, elite wheat genotypes were crossed using a chemical hybridizing agent at different doses. A total of 23 hybrids were developed from a partial diallel design; and planted in an alpha lattice design with their parents at two locations in Morocco, for two years, to evaluate for yield components, heterosis and combining abilities. The 13.5 L ha⁻¹ dose induced a maximum level of sterility (95%) and seed set showed large phenotypic variation and high heritability. In parallel, seed set showed tight correlation with pollen mass (0.97), visual anther extrusion (0.94) and pollen shedding (0.91) (p < 0.001), allowing direct selection of the associated traits. Using the combined data, mid-parent heterosis ranges were −7.64–14.55% for biomass (BM), −8.34–12.51% for thousand kernel weight (TKW) and −5.29–26.65% for grain yield (YLD); while best-parent heterosis showed ranges of −11.18–7.20%, −11.35–11.26% and −8.27–24.04% for BM, TKW and YLD, respectively. The magnitude of general combining ability (GCA) variance was greater than the specific combining ability (SCA) variance suggesting a greater additive gene action for BM, TKW and YLD. The favorable GCA estimates showed a simple method to predict additive effects contributing to high heterosis and thus could be an effective approach for the selection of promising parents in early generations. Full article

(This article belongs to the Special Issue Wheat Breeding, Genomic Selection, and Phenomics)

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15 pages, 2283 KiB

Open AccessArticle

Genetic and Morpho-Agronomic Characterization of Sicilian Tetraploid Wheat Germplasm

by Angelo Sicilia, Umberto Anastasi, Michele Bizzini, Stefania Montemagno, Carmelo Nicotra, Sebastiano Blangiforti, Alfio Spina, Salvatore Luciano Cosentino and Angela Roberta Lo Piero

Plants 2022, 11(1), 130; https://0-doi-org.brum.beds.ac.uk/10.3390/plants11010130 - 04 Jan 2022

Cited by 8 | Viewed by 1825

Abstract

Cereal landraces are a very valuable resource in contemporary agriculture. A renewed focus for breeding purposes could ameliorate some negative consequences of modern agriculture and conventional breeding, such as the loss of genetic diversity. One strategy combining molecular genotyping and characterization of morpho-agronomic traits related to productivity is proposed to assess a group of tetraploid wheat landraces named Bufala, historically cultivated in the mountain areas of Sicily and characterized by adaptability in terms of cold tolerance, ability to grow in marginal soils, weed competitiveness and resistance to diseases. A total of 55 SSR molecular markers were used to detect patterns of diversity in 30 rivet and durum wheat genotypes. Furthermore, phenotyping was then conducted for 8 morpho-agronomic traits. Discriminant analysis of principal components (DAPC), STRUCTURE and phylogenetical analysis allowed to identify three groups, two of them genetically close and including both Bufala and Bufala-related rivet landraces. To the third group, old and more recent durum wheat varieties, constituting the outgroup, were assigned. Clustering was confirmed by Principal Component Analysis (PCA). Finally, a correlation analysis showed that Bufala genotypes are characterized by lower ear density, major ear length and later earing time compared with the other studied genotypes. The levels of diversity and population structure could be an important contribution to parent selection in tetraploid wheat breeding programs, as well as to germplasm conservation and management. Full article

(This article belongs to the Special Issue Wheat Breeding, Genomic Selection, and Phenomics)

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16 pages, 1668 KiB

Open AccessArticle

Genome-Wide Association of Stem Carbohydrate Accumulation and Remobilization during Grain Growth in Bread Wheat (Triticum aestivum L.) in Mediterranean Environments

by Fernando P. Guerra, Alejandra Yáñez, Iván Matus and Alejandro del Pozo

Plants 2021, 10(3), 539; https://0-doi-org.brum.beds.ac.uk/10.3390/plants10030539 - 12 Mar 2021

Cited by 2 | Viewed by 2000

Abstract

Water deficit represents an important challenge for wheat production in many regions of the world. Accumulation and remobilization of water-soluble carbohydrates (WSCs) in stems are part of the physiological responses regulated by plants to cope with water stress and, in turn, determine grain yield (GY). The genetic mechanisms underlying the variation in WSC are only partially understood. In this study, we aimed to identify Single Nucleotide Polymorphism (SNP) markers that account for variation in a suite of WSC and GY, evaluated in 225 cultivars and advanced lines of spring wheat. These genotypes were established in two sites in the Mediterranean region of Central Chile, under water-limited and full irrigation conditions, and assessed in two growing seasons, namely anthesis and maturity growth periods. A genome-wide association study (GWAS) was performed by using 3243 SNP markers. Genetic variance accounted for 5 to 52% of phenotypic variation of the assessed traits. A rapid linkage disequilibrium decay was observed across chromosomes (r² ≤ 0.2 at 2.52 kbp). Marker-trait association tests identified 96 SNPs related to stem weight (SW), WSCs, and GY, among other traits, at the different sites, growing seasons, and growth periods. The percentage of SNPs that were part of the gene-coding regions was 34%. Most of these genes are involved in the defensive response to drought and biotic stress. A complimentary analysis detected significant effects of different haplotypes on WSC and SW, in anthesis and maturity. Our results evidence both genetic and environmental influence on WSC dynamics in spring wheat. At the same time, they provide a series of markers suitable for supporting assisted selection approaches and functional characterization of genes. Full article

(This article belongs to the Special Issue Wheat Breeding, Genomic Selection, and Phenomics)

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Review

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32 pages, 551 KiB

Open AccessEditor’s ChoiceReview

Genetic Improvement of Wheat for Drought Tolerance: Progress, Challenges and Opportunities

by Theresa Bapela, Hussein Shimelis, Toi John Tsilo and Isack Mathew

Plants 2022, 11(10), 1331; https://0-doi-org.brum.beds.ac.uk/10.3390/plants11101331 - 18 May 2022

Cited by 32 | Viewed by 9412

Abstract

Wheat production and productivity are challenged by recurrent droughts associated with climate change globally. Drought and heat stress resilient cultivars can alleviate yield loss in marginal production agro-ecologies. The ability of some crop genotypes to thrive and yield in drought conditions is attributable to the inherent genetic variation and environmental adaptation, presenting opportunities to develop drought-tolerant varieties. Understanding the underlying genetic, physiological, biochemical, and environmental mechanisms and their interactions is key critical opportunity for drought tolerance improvement. Therefore, the objective of this review is to document the progress, challenges, and opportunities in breeding for drought tolerance in wheat. The paper outlines the following key aspects: (1) challenges associated with breeding for adaptation to drought-prone environments, (2) opportunities such as genetic variation in wheat for drought tolerance, selection methods, the interplay between above-ground phenotypic traits and root attributes in drought adaptation and drought-responsive attributes and (3) approaches, technologies and innovations in drought tolerance breeding. In the end, the paper summarises genetic gains and perspectives in drought tolerance breeding in wheat. The review will serve as baseline information for wheat breeders and agronomists to guide the development and deployment of drought-adapted and high-performing new-generation wheat varieties. Full article

(This article belongs to the Special Issue Wheat Breeding, Genomic Selection, and Phenomics)

10 pages, 1335 KiB

Open AccessReview

The Evaluation of Winter Wheat Adaptation to Climate Change in the Central Non-Black Region of Russia: Study of the Gene Pool Resistance of Wheat from the N.I. Vavilov Institute of Plant Industry (VIR) World Collection to Abiotic Stress Factors

by Sulukhan K. Temirbekova, Ivan M. Kulikov, Yuliya V. Afanasyeva, Olga O. Beloshapkina, Elena A. Kalashnikova, Rima N. Kirakosyan, Peter A. Dokukin, Dmitry E. Kucher, Mourad Latati and Nazih Y. Rebouh

Plants 2021, 10(11), 2337; https://0-doi-org.brum.beds.ac.uk/10.3390/plants10112337 - 29 Oct 2021

Cited by 8 | Viewed by 2250

Abstract

The paper presents the results of a 50-year research of the genepool of the winter wheat from the world’s largest wheat collection of N.I. Vavilov Institute of Plant Industry (VIR) to investigate its resistance to the abiotic stress factors of the Moscow region and see how closely it matches the attributes of a wheat ideotype as postulated by N.I. Vavilov in 1935. The critical years in studying the wheat’s winter resistance were 10 years out of 50: excessive water saturation during the year 2013; soil drought in 1988; and atmospheric drought in 1972 and 2010. During the investigation, the following gene pool features were analyzed: frost characterized by the cultivar Sojuz 50 (Russia), rapid temperature change, thawing, ice, and rotting resistance characterized by the cultivars Zarya 2 (Russia), Sv 75268, (Sweden), Caristerm and Tukan (Germany), PP 114-74 and Liwilla (Poland), Maris Ploughman and Granta (Great Britain), Titan (USA), Zdar (Czech), and Zenta (Switzerland); regeneration capacity in spring after poor wintering expressed by the cultivars Pamyati Fedina (Russia), TAW 3668.71 (Germany) and Rmo (Poland); resistance to excessive soil and air saturation exhibited by the cultivars Moskovskaya 39 (Russia), Tukan, Compal, Obelisk, Orestis, and Bussard (Germany); solid standing culm that is resistant to lodging characterized by the cultivars Tukan, Kronjuwel, Compal (Germany), Zenta (Switzerland), Moskovskaya 56 (Russia), and Hvede Sarah (Denmark); resistance to enzyme-mycotic depletion of seeds characterized by the cultivars Tukan, Compal, Obelisk, Orestis, Bussard (Germany), Sv 75268, Helge, VG 73394, Salut, Sv 75355 (Sweden), Zenta (Switzerland), Moskovskaya 39, and Ferrugineum 737.76 (Russia); and resistance to soil and atmospheric drought demonstrated by the cultivars Liessau, Heine Stamm, Severin, Neuzucht 14/4, Haynes, Rus 991, Halle 1020 (Germany), Gama (Poland), Sv 71536 (Sweden), and Moskovskaya 39 (Russia). Moreover, the cultivar Mironovskaya 808 (Ukraine) showed resistance to almost all abiotic stress factors studied. The performed study contributes towards the provision of potential sources of resistance to abiotic stress factors prevalent in the Moscow region that can be incorporated in advanced breeding programs. Full article

(This article belongs to the Special Issue Wheat Breeding, Genomic Selection, and Phenomics)

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