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A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Plant Genetics and Genomics".

Deadline for manuscript submissions: closed (20 March 2023) | Viewed by 34751

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Prof. Dr. Hongxiang Ma

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College of Agricultural, Yangzhou University, Yangzhou 225809, China
Interests: genetics; genomics; molecular biology; molecular cytogenetics; molecular breeding; plant biotechnology; wheat
Special Issues, Collections and Topics in MDPI journals

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Dear Colleagues,

Wheat is one of the most important cereal crops in the world and the main source of food for roughly one-third of the world’s population. Breeding for improved agronomic performance, resistance to biotic and abiotic stress, high yield potential, and desirable quality in wheat is necessary to promote the sustainable development of the wheat industry and ensure food security and safety worldwide.

Genetic studies are the basis of wheat breeding. In recent years, high-quality annotation of wheat as well as the development of other newly emerging technologies in biological sciences, i.e., next-generation sequencing, omics technologies, and genome editing techniques, advances fundamental genetic research in wheat. These new advances in molecular development will help to determine the wheat genetic diversity, identify novel QTL/genes, reveal genotypic interactions with the environment, and to develop new breeding techniques for wheat varieties.

This Special Issue welcomes original research articles in addition to reviews and opinions about the genetic diversity and evolution, gene discovery, function and molecular mechanism, omics studies, molecular breeding, genome editing, and other new progress related to wheat genetics.

Dr. Hongxiang Ma
Guest Editor

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Keywords

wheat
genetics
molecular mapping
gene function
gene regulation
omics
genetic modification
molecular breeding

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Published Papers (12 papers)

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Editorial

Jump to: Research, Review

4 pages, 196 KiB

Open AccessEditorial

Editorial for the Special Issue “Genetics Studies on Wheat”

by Hongxiang Ma

Genes 2023, 14(9), 1761; https://doi.org/10.3390/genes14091761 - 4 Sep 2023

Cited by 1 | Viewed by 962

Abstract

Wheat (Triticum aestivum L [...] Full article

(This article belongs to the Special Issue Genetics Studies on Wheat)

Research

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21 pages, 4188 KiB

Open AccessArticle

Genetic Diversity of Durum Wheat (Triticum turgidum L. ssp. durum, Desf) Germplasm as Revealed by Morphological and SSR Markers

by Temesgen Dagnaw, Behailu Mulugeta, Teklehaimanot Haileselassie, Mulatu Geleta, Rodomiro Ortiz and Kassahun Tesfaye

Genes 2023, 14(6), 1155; https://doi.org/10.3390/genes14061155 - 26 May 2023

Cited by 10 | Viewed by 3972

Abstract

Ethiopia is considered a center of origin and diversity for durum wheat and is endowed with many diverse landraces. This research aimed to estimate the extent and pattern of genetic diversity in Ethiopian durum wheat germplasm. Thus, 104 durum wheat genotypes representing thirteen populations, three regions, and four altitudinal classes were investigated for their genetic diversity, using 10 grain quality- and grain yield-related phenotypic traits and 14 simple sequence repeat (SSR) makers. The analysis of the phenotypic traits revealed a high mean Shannon diversity index (H′ = 0.78) among the genotypes and indicated a high level of phenotypic variation. The principal component analysis (PCA) classified the genotypes into three groups. The SSR markers showed a high mean value of polymorphic information content (PIC = 0.50) and gene diversity (h = 0.56), and a moderate number of alleles per locus (Na = 4). Analysis of molecular variance (AMOVA) revealed a high level of variation within populations, regions, and altitudinal classes, accounting for 88%, 97%, and 97% of the total variation, respectively. Pairwise genetic differentiation and Nei’s genetic distance analyses identified that the cultivars are distinct from the landrace populations. The distance-based (Discriminant Analysis of Principal Component (DAPC) and Minimum Spanning Network (MSN)) and model-based population stratification (STRUCTURE) methods of clustering grouped the genotypes into two clusters. Both the phenotypic data-based PCA and the molecular data-based DAPC and MSN analyses defined distinct groupings of cultivars and landraces. The phenotypic and molecular diversity analyses highlighted the high genetic variation in the Ethiopian durum wheat gene pool. The investigated SSRs showed significant associations with one or more target phenotypic traits. The markers identify landraces with high grain yield and quality traits. This study highlights the usefulness of Ethiopian landraces for cultivar development, contributing to food security in the region and beyond. Full article

(This article belongs to the Special Issue Genetics Studies on Wheat)

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11 pages, 1523 KiB

Open AccessArticle

Genome-Wide Association Analysis of Grain Hardness in Common Wheat

by Xianfang He, Maoang Lu, Jiajia Cao, Xu Pan, Jie Lu, Li Zhao, Haiping Zhang, Cheng Chang, Jianlai Wang and Chuanxi Ma

Genes 2023, 14(3), 672; https://doi.org/10.3390/genes14030672 - 8 Mar 2023

Cited by 3 | Viewed by 1927

Abstract

The grain hardness index (HI) is one of the important reference bases for wheat quality and commodity properties; therefore, it is essential and useful to identify loci associated with the HI in wheat breeding. The grain hardness index of the natural population including 150 common wheat genotypes was measured in this study. The phenotypic data diversity of HI based on four environments and the best linear unbiased prediction (BLUP) was analyzed. The results showed that the grain HI of the natural population ranged from 15.00 to 83.00, the variation range was from 5.10% to 24.44%, and the correlation coefficient was 0.872–0.980. BLUP value was used to grade and assign the grain HI to hard wheat, mixed wheat, and soft wheat, and the assigned phenotypes were used for genome-wide association analysis. Two types of grain hardness index phenotypic values were used for genome-wide association analysis (GWAS) using a 55K SNP array. A total of five significant association loci (p < 0.001) were excavated, among which four loci could be detected in three or more environments. They were distributed on chromosomes 1A and 7D, and the phenotypic contribution rate was 7.52% to 10.66%. A total of 48 sites related to grain hardness were detected by the assignment method, among which five were stable genetic sites, distributed on chromosomes 1A(2), 3B(1), 4B(1), and 7D(1), with phenotypic contribution rates ranging from 7.63% to 11.12%. Of the five loci detected by the assignment method, two stable loci were co-located in the phenotypic mapping results of the hardness index. One of the loci was consistent with previous reports and located on chromosome 1A, and one locus was unreported on chromosome 7D. Therefore, it may be a feasible attempt to use the assignment method to conduct genome-wide association analysis of the grain hardness index. In this study, a total of five genetic loci for grain hardness stability were excavated, and two of the loci were located in the two phenotypic values, two of which were not reported. Full article

(This article belongs to the Special Issue Genetics Studies on Wheat)

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13 pages, 1748 KiB

Open AccessArticle

Transfer of the Resistance to Multiple Diseases from a Triticum-Secale-Thinopyrum Trigeneric Hybrid to Ningmai 13 and Yangmai 23 Wheat Using Specific Molecular Markers and GISH

by Yi Dai, Juntao Shi, Jinfeng Li, Yujiao Gao, Haigang Ma, Yonggang Wang, Baotong Wang, Jianmin Chen, Peng Cheng and Hongxiang Ma

Genes 2022, 13(12), 2345; https://doi.org/10.3390/genes13122345 - 12 Dec 2022

Cited by 3 | Viewed by 1626

Abstract

The middle to lower reaches of the Yangtze River are China’s second largest area for wheat production; wheat disease is more serious there than in other areas because of the high humidity and warm weather. However, most cultivated varieties are susceptible to Fusarium head blight (FHB), powdery mildew, and stripe rust, and the lack of disease-resistant germplasm is an obstacle in wheat breeding. Rye and Thinopyrum elongatum, related species of wheat, carry many genes involved in disease resistance. In this study, a trigeneric hybrid, YZU21, with resistance to FHB, powdery mildew, and stripe rust was used to improve two major wheat cultivars, Ningmai 13 (NM13) and Yangmai 23 (YM23). Specific molecular markers and GISH were used to identify hybrid progenies. Five addition or substitution lines and one translocation line of the Triticum-Secale-Thinopyrum trigeneric hybrid were obtained and evaluated for agronomic traits and the resistance to multiple diseases. The results showed that the six trigeneric hybrid lines had desirable agronomic traits and improved resistance to FHB, powdery mildew, and stripe rust; they might be used as parents in wheat breeding for the resistance to multiple disease. Full article

(This article belongs to the Special Issue Genetics Studies on Wheat)

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19 pages, 1645 KiB

Open AccessArticle

Genome-Wide Association Study for Spot Blotch Resistance in Synthetic Hexaploid Wheat

by Nerida Lozano-Ramirez, Susanne Dreisigacker, Carolina P. Sansaloni, Xinyao He, José Sergio Sandoval-Islas, Paulino Pérez-Rodríguez, Aquiles Carballo Carballo, Cristian Nava Diaz, Masahiro Kishii and Pawan K. Singh

Genes 2022, 13(8), 1387; https://doi.org/10.3390/genes13081387 - 4 Aug 2022

Cited by 7 | Viewed by 2385

Abstract

Spot blotch (SB) caused by Bipolaris sorokiniana (Sacc.) Shoem is a destructive fungal disease affecting wheat and many other crops. Synthetic hexaploid wheat (SHW) offers opportunities to explore new resistance genes for SB for introgression into elite bread wheat. The objectives of our study were to evaluate a collection of 441 SHWs for resistance to SB and to identify potential new genomic regions associated with the disease. The panel exhibited high SB resistance, with 250 accessions showing resistance and 161 showing moderate resistance reactions. A genome-wide association study (GWAS) revealed a total of 41 significant marker–trait associations for resistance to SB, being located on chromosomes 1B, 1D, 2A, 2B, 2D, 3A, 3B, 3D, 4A, 4D, 5A, 5D, 6D, 7A, and 7D; yet none of them exhibited a major phenotypic effect. In addition, a partial least squares regression was conducted to validate the marker–trait associations, and 15 markers were found to be most important for SB resistance in the panel. To our knowledge, this is the first GWAS to investigate SB resistance in SHW that identified markers and resistant SHW lines to be utilized in wheat breeding. Full article

(This article belongs to the Special Issue Genetics Studies on Wheat)

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14 pages, 5074 KiB

Open AccessArticle

Characterization of Expression and Epigenetic Features of Core Genes in Common Wheat

by Dongyang Zheng and Wenli Zhang

Genes 2022, 13(7), 1112; https://doi.org/10.3390/genes13071112 - 21 Jun 2022

Cited by 1 | Viewed by 2180

Abstract

The availability of multiple wheat genome sequences enables us to identify core genes and characterize their genetic and epigenetic features, thereby advancing our understanding of their biological implications within individual plant species. It is, however, largely understudied in wheat. To this end, we reanalyzed genome sequences from 16 different wheat varieties and identified 62,299 core genes. We found that core and non-core genes have different roles in subgenome differentiation. Meanwhile, according to their expression profiles, these core genes can be classified into genes related to tissue development and stress responses, including 3376 genes highly expressed in both spikelets and at high temperatures. After associating with six histone marks and open chromatin, we found that these core genes can be divided into eight sub-clusters with distinct epigenomic features. Furthermore, we found that ca. 51% of the expressed transcription factors (TFs) were marked with both H3K27me3 and H3K4me3, indicative of the bivalency feature, which can be involved in tissue development through the TF-centered regulatory network. Thus, our study provides a valuable resource for the functional characterization of core genes in stress responses and tissue development in wheat. Full article

(This article belongs to the Special Issue Genetics Studies on Wheat)

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10 pages, 1605 KiB

Open AccessArticle

Genome-Wide Association Mapping of Grain Metal Accumulation in Wheat

by Mohamed El-Soda and Maha Aljabri

Genes 2022, 13(6), 1052; https://doi.org/10.3390/genes13061052 - 13 Jun 2022

Cited by 11 | Viewed by 2601

Abstract

Increasing wheat grain yield while ignoring grain quality and metal accumulation can result in metal deficiencies, particularly in countries where bread wheat accounts for the majority of daily dietary regimes. When the accumulation level exceeds a certain threshold, it becomes toxic and causes various diseases. Biofortification is an effective method of ensuring nutritional security. We screened 200 spring wheat advanced lines from the wheat association mapping initiative for Mn, Fe, Cu, Zn, Ni, and Cd concentrations. Interestingly, high-yielding genotypes had high essential metals, such as Mn, Fe, Cu, and Zn, but low levels of toxic metals, such as Ni and Cd. Positive correlations were found between all metals except Ni and Cd, where no correlation was found. We identified 142 significant SNPs, 26 of which had possible pleiotropic effects on two or more metals. Several QTLs co-located with previously mapped QTL for the same or other metals, whereas others were new. Our findings contribute to wheat genetic biofortification through marker-assisted selection, ensuring nutritional security in the long run. Full article

(This article belongs to the Special Issue Genetics Studies on Wheat)

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10 pages, 2213 KiB

Open AccessArticle

ATP-dependent DNA helicase (TaDHL), a Novel Reduced-Height (Rht) Gene in Wheat

by Baojin Guo, Xuemei Jin, Jingchuan Chen, Huiyan Xu, Mingxia Zhang, Xing Lu, Rugang Wu, Yan Zhao, Ying Guo, Yanrong An and Sishen Li

Genes 2022, 13(6), 979; https://doi.org/10.3390/genes13060979 - 30 May 2022

Cited by 9 | Viewed by 3859

Abstract

In wheat, a series of dwarf and semi-dwarf plant varieties have been developed and utilized worldwide since the 1960s and caused the ‘Green Revolution’. To date, 25 reduced-height (Rht) genes have been identified, but only several genes for plant height (PH) have been isolated previously. In this study, we identified a candidate gene, ATP-dependent DNA helicase (TaDHL-7B), for PH via QTL mapping and genome-wide association study (GWAS) methods. We knocked out this gene using the CRISPR/Cas9 system in variety ‘Fielder’. Two homozygous mutant genotypes, AAbbDD (−5 bp) and AAbbDD (−1 bp), were obtained in the T₂ generation. The PH values of AAbbDD (−5 bp) and AAbbDD (−1 bp) were significantly reduced compared with the wild-type (WT, ‘Fielder’), indicating that TaDHL-7B is a novel Rht gene that controls the PH. This is the first time that a PH gene of wheat has been isolated with a non-hormone pathway, providing a new insight into the genetic control of PH. The TaDHL gene reduced the PH without a yield penalty. It could be used to improve the lodging resistance and yield in wheat breeding programs. Full article

(This article belongs to the Special Issue Genetics Studies on Wheat)

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16 pages, 2276 KiB

Open AccessArticle

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

by Rahul M. Phuke, Xinyao He, Philomin Juliana, Muhammad R. Kabir, Krishna K. Roy, Felix Marza, Chandan Roy, Gyanendra P. Singh, Aakash Chawade, Arun K. Joshi and Pawan K. Singh

Genes 2022, 13(4), 596; https://doi.org/10.3390/genes13040596 - 27 Mar 2022

Cited by 7 | Viewed by 3388

Abstract

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. Full article

(This article belongs to the Special Issue Genetics Studies on Wheat)

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19 pages, 7165 KiB

Open AccessArticle

Role of Wheat Phosphorus Starvation Tolerance 1 Genes in Phosphorus Acquisition and Root Architecture

by Hina Abbas, Muhammad Kashif Naeem, Marya Rubab, Emilie Widemann, Muhammad Uzair, Nageen Zahra, Bilal Saleem, Amna Abdul Rahim, Safeena Inam, Muhammad Imran, Farhan Hafeez, Muhammad Ramzan Khan and Sarfraz Shafiq

Genes 2022, 13(3), 487; https://doi.org/10.3390/genes13030487 - 10 Mar 2022

Cited by 8 | Viewed by 3761

Abstract

The wheat plant requires elevated phosphorus levels for its normal growth and yield, but continuously depleting non-renewable phosphorus reserves in the soil is one of the biggest challenges in agricultural production worldwide. The Phosphorus Starvation Tolerance 1 (PSTOL1) gene has been reported to play a key role in efficient P uptake, deeper rooting, and high yield in rice. However, the function of the PSTOL1 gene in wheat is still unclear. In this study, a total of 22 PSTOL1 orthologs were identified in the wheat genome, and found that wheat PSTOL1 orthologs are unevenly distributed on chromosomes, and these genes were under strong purifying selection. Under different phosphorus regimes, wheat PSTOL1 genes showed differential expression patterns in different tissues. These results strengthen the classification of Pakistan-13 as a P-efficient cultivar and Shafaq-06 as a P-inefficient cultivar. Phenotypic characterization demonstrated that Pakistan-13 wheat cultivar has significantly increased P uptake, root length, root volume, and root surface area compared to Shafaq-06. Some wheat PSTOL1 orthologs are co-localized with phosphorus starvation’s related quantitative trait loci (QTLs), suggesting their potential role in phosphorus use efficiency. Altogether, these results highlight the role of the wheat PSTOL1 genes in wheat P uptake, root architecture, and efficient plant growth. This comprehensive study will be helpful for devising sustainable strategies for wheat crop production and adaptation to phosphorus insufficiency. Full article

(This article belongs to the Special Issue Genetics Studies on Wheat)

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Review

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11 pages, 262 KiB

Open AccessReview

Genetic Improvement of Wheat with Pre-Harvest Sprouting Resistance in China

by Cheng Chang, Haiping Zhang, Jie Lu, Hongqi Si and Chuanxi Ma

Genes 2023, 14(4), 837; https://doi.org/10.3390/genes14040837 - 30 Mar 2023

Cited by 7 | Viewed by 2610

Abstract

Wheat pre-harvest sprouting (PHS) refers to the germination of seeds directly on the spike due to rainy weather before harvest, which often results in yield reduction, quality deterioration, and seed value loss. In this study, we reviewed the research progress in the quantitative trait loci (QTL) detection and gene excavation related to PHS resistance in wheat. Simultaneously, the identification and creation of germplasm resources and the breeding of wheat with PHS resistance were expounded in this study. Furthermore, we also discussed the prospect of molecular breeding during genetic improvement of PHS-resistant wheat. Full article

(This article belongs to the Special Issue Genetics Studies on Wheat)

13 pages, 2515 KiB

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Genetic Improvement and Application Practices of Synthetic Hexaploid Wheat

by Hongshen Wan, Fan Yang, Jun Li, Qin Wang, Zehou Liu, Yonglu Tang and Wuyun Yang

Genes 2023, 14(2), 283; https://doi.org/10.3390/genes14020283 - 21 Jan 2023

Cited by 9 | Viewed by 2875

Abstract

Synthetic hexaploid wheat (SHW) is a useful genetic resource that can be used to improve the performance of common wheat by transferring favorable genes from a wide range of tetraploid or diploid donors. From the perspectives of physiology, cultivation, and molecular genetics, the use of SHW has the potential to increase wheat yield. Moreover, genomic variation and recombination were enhanced in newly formed SHW, which could generate more genovariation or new gene combinations compared to ancestral genomes. Accordingly, we presented a breeding strategy for the application of SHW—the ‘large population with limited backcrossing method’—and we pyramided stripe rust resistance and big-spike-related QTLs/genes from SHW into new high-yield cultivars, which represents an important genetic basis of big-spike wheat in southwestern China. For further breeding applications of SHW-derived cultivars, we used the ‘recombinant inbred line-based breeding method’ that combines both phenotypic and genotypic evaluations to pyramid multi-spike and pre-harvest sprouting resistance QTLs/genes from other germplasms to SHW-derived cultivars; consequently, we created record-breaking high-yield wheat in southwestern China. To meet upcoming environmental challenges and continuous global demand for wheat production, SHW with broad genetic resources from wild donor species will play a major role in wheat breeding. Full article

(This article belongs to the Special Issue Genetics Studies on Wheat)

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