Wheat Genomics, Genetics and Breeding

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

Deadline for manuscript submissions: closed (25 May 2023) | Viewed by 10954

Special Issue Editors


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Guest Editor
National Agri-Food Biotechnology Institute (NABI), Mohali, India
Interests: wheat; genetics; anthocyanins; phenolics; genomics

E-Mail Website
Guest Editor
National Agri-Food Biotechnology Institute (NABI), Mohali, India
Interests: wheat; genetics; anthocyanins; phenolics; genomics; animal model studies

E-Mail Website
Guest Editor
National Agri-Food Biotechnology Institute (NABI), Mohali, India
Interests: wheat; genetics; genomics; bioinformatics

Special Issue Information

Dear Colleagues,

Global food security faces multiple challenges, including climate change, declining natural resources, emerging human/animal and plant diseases, persistent hunger, and malnutrition. By 2050, demand for wheat is predicted to increase by 50 percent from today’s levels. Meanwhile, the crop is at risk from new and more aggressive pests as well as diseases, diminishing water resources, limited available land, and unstable weather conditions, particularly heat. Abiotic and biotic stresses, processing, and nutritional quality are all considered in classical breeding and metabolite characterization. Recent advances in genomics research have transformed crop improvement strategies, allowing scientists to undertake speed breeding strategies to introduce premium grain quality and nutritional traits. The unprecedented recent developments in next-generation DNA sequencing technologies and high-density genotyping-based trait mapping, such as QTL discovery, fine mapping, pooled sequencing (QTLseq, BSRseq, MutMap, etc.), genome-wide association studies, and systems genetics tools allow for the discovery of superior haplotypes to enhance the nutritional content of a wide array of crops. Therefore, this Special Issue of Genes is focused on wheat genomics, genetics, and breeding, with the goal of contributing to food and nutrition security; climate adaption and mitigation; and the development of climate-resilient, nutritious, disease- and pest-tolerant, diverse, and high-yielding wheat varieties. This effort incorporates the use of genomic selection platforms, systems biology, genome-editing tools, wide introgression to exploit genetic variation in wild relatives of wheat, the domestication of wheat, genetic diversity, genomics, functional genomics, transcriptomics, and biosynthetic as well as regulatory genes. We believe that the whole wheat community will find this compilation helpful. 

Dr. Monika Garg
Dr. Saloni Sharma
Dr. Apoorv Tiwari
Guest Editors

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Keywords

  • wheat
  • genetics
  • genomics

Published Papers (5 papers)

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Research

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11 pages, 614 KiB  
Article
QTL Mapping and Candidate Gene Identifying for N, P, and K Use Efficiency at the Maturity Stages in Wheat
by Xu Han, Mingxia Zhang, Minggang Gao, Yuanyuan Yuan, Yapei Yuan, Guizhi Zhang, Yanrong An, Ying Guo, Fanmei Kong and Sishen Li
Genes 2023, 14(6), 1168; https://doi.org/10.3390/genes14061168 - 27 May 2023
Viewed by 1338
Abstract
Nitrogen (N), phosphorus (P), and potassium (K) are the three most important mineral nutrients for crop growth and development. We previously constructed a genetic map of unigenes (UG-Map) based on their physical positions using a RIL population derived from the cross of “TN18 [...] Read more.
Nitrogen (N), phosphorus (P), and potassium (K) are the three most important mineral nutrients for crop growth and development. We previously constructed a genetic map of unigenes (UG-Map) based on their physical positions using a RIL population derived from the cross of “TN18 × LM6” (TL-RILs). In this study, a total of 18 traits related to mineral use efficiency (MUE) of N/P/K were investigated under three growing seasons using TL-RILs. A total of 54 stable QTLs were detected, distributed across 19 chromosomes except for 3A and 5B. There were 50 QTLs associated with only one trait, and the other four QTLs were associated with two traits. A total of 73 candidate genes for stable QTLs were identified. Of these, 50 candidate genes were annotated in Chinese Spring (CS) RefSeq v1.1. The average number of candidate genes per QTL was 1.35, with 45 QTLs containing only one candidate gene and nine QTLs containing two or more candidate genes. The candidate gene TraesCS6D02G132100 (TaPTR gene) for QGnc-6D-3306 belongs to the NPF (NRT1/PTR) gene family. We speculate that the TaPTR gene should regulate the GNC trait. Full article
(This article belongs to the Special Issue Wheat Genomics, Genetics and Breeding)
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20 pages, 4154 KiB  
Article
Genome–Transcriptome Transition Approaches to Characterize Anthocyanin Biosynthesis Pathway Genes in Blue, Black and Purple Wheat
by Payal Kapoor, Saloni Sharma, Apoorv Tiwari, Satveer Kaur, Anita Kumari, Humira Sonah, Ajay Goyal, Meena Krishania and Monika Garg
Genes 2023, 14(4), 809; https://doi.org/10.3390/genes14040809 - 27 Mar 2023
Cited by 3 | Viewed by 1863
Abstract
Colored wheat has gained enormous attention from the scientific community, but the information available on the anthocyanin biosynthetic genes is very minimal. The study involved their genome-wide identification, in silico characterization and differential expression analysis among purple, blue, black and white wheat lines. [...] Read more.
Colored wheat has gained enormous attention from the scientific community, but the information available on the anthocyanin biosynthetic genes is very minimal. The study involved their genome-wide identification, in silico characterization and differential expression analysis among purple, blue, black and white wheat lines. The recently released wheat genome mining putatively identified eight structural genes in the anthocyanin biosynthesis pathway with a total of 1194 isoforms. Genes showed distinct exon architecture, domain profile, regulatory elements, chromosome emplacement, tissue localization, phylogeny and synteny, indicative of their unique function. RNA sequencing of developing seeds from colored (black, blue and purple) and white wheats identified differential expressions in 97 isoforms. The F3H on group two chromosomes and F3′5′H on 1D chromosomes could be significant influencers in purple and blue color development, respectively. Apart from a role in anthocyanin biosynthesis, these putative structural genes also played an important role in light, drought, low temperature and other defense responses. The information can assist in targeted anthocyanin production in the wheat seed endosperm. Full article
(This article belongs to the Special Issue Wheat Genomics, Genetics and Breeding)
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18 pages, 2814 KiB  
Article
Genome-Wide Association Study for Grain Protein, Thousand Kernel Weight, and Normalized Difference Vegetation Index in Bread Wheat (Triticum aestivum L.)
by Gopalareddy Krishnappa, Hanif Khan, Hari Krishna, Narayana Bhat Devate, Satish Kumar, Chandra Nath Mishra, Om Parkash, Sachin Kumar, Monu Kumar, Harohalli Masthigowda Mamrutha, Gyanendra Pratap Singh and Gyanendra Singh
Genes 2023, 14(3), 637; https://doi.org/10.3390/genes14030637 - 3 Mar 2023
Cited by 4 | Viewed by 2106
Abstract
Genomic regions governing grain protein content (GPC), 1000 kernel weight (TKW), and normalized difference vegetation index (NDVI) were studied in a set of 280 bread wheat genotypes. The genome-wide association (GWAS) panel was genotyped using a 35K Axiom array and phenotyped in three [...] Read more.
Genomic regions governing grain protein content (GPC), 1000 kernel weight (TKW), and normalized difference vegetation index (NDVI) were studied in a set of 280 bread wheat genotypes. The genome-wide association (GWAS) panel was genotyped using a 35K Axiom array and phenotyped in three environments. A total of 26 marker-trait associations (MTAs) were detected on 18 chromosomes covering the A, B, and D subgenomes of bread wheat. The GPC showed the maximum MTAs (16), followed by NDVI (6), and TKW (4). A maximum of 10 MTAs was located on the B subgenome, whereas, 8 MTAs each were mapped on the A and D subgenomes. In silico analysis suggest that the SNPs were located on important putative candidate genes such as NAC domain superfamily, zinc finger RING-H2-type, aspartic peptidase domain, folylpolyglutamate synthase, serine/threonine-protein kinase LRK10, pentatricopeptide repeat, protein kinase-like domain superfamily, cytochrome P450, and expansin. These candidate genes were found to have different roles including regulation of stress tolerance, nutrient remobilization, protein accumulation, nitrogen utilization, photosynthesis, grain filling, mitochondrial function, and kernel development. The effects of newly identified MTAs will be validated in different genetic backgrounds for further utilization in marker-aided breeding. Full article
(This article belongs to the Special Issue Wheat Genomics, Genetics and Breeding)
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16 pages, 4465 KiB  
Article
Molecular Mapping of Biofortification Traits in Bread Wheat (Triticum aestivum L.) Using a High-Density SNP Based Linkage Map
by Vasudha Jadon, Shashi Sharma, Hari Krishna, Gopalareddy Krishnappa, Rahul Gajghate, Narayana Bhat Devate, Kusuma Kumari Panda, Neelu Jain, Pradeep Kumar Singh and Gyanendra Pratap Singh
Genes 2023, 14(1), 221; https://doi.org/10.3390/genes14010221 - 14 Jan 2023
Cited by 4 | Viewed by 2097
Abstract
A set of 188 recombinant inbred lines (RILs) derived from a cross between a high-yielding Indian bread wheat cultivar HD2932 and a synthetic hexaploid wheat (SHW) Synthetic 46 derived from tetraploid Triticum turgidum (AA, BB 2n = 28) and diploid Triticum tauschii (DD, [...] Read more.
A set of 188 recombinant inbred lines (RILs) derived from a cross between a high-yielding Indian bread wheat cultivar HD2932 and a synthetic hexaploid wheat (SHW) Synthetic 46 derived from tetraploid Triticum turgidum (AA, BB 2n = 28) and diploid Triticum tauschii (DD, 2n = 14) was used to identify novel genomic regions associated in the expression of grain iron concentration (GFeC), grain zinc concentration (GZnC), grain protein content (GPC) and thousand kernel weight (TKW). The RIL population was genotyped using SNPs from 35K Axiom® Wheat Breeder’s Array and 34 SSRs and phenotyped in two environments. A total of nine QTLs including five for GPC (QGpc.iari_1B, QGpc.iari_4A, QGpc.iari_4B, QGpc.iari_5D, and QGpc.iari_6B), two for GFeC (QGfec.iari_5B and QGfec.iari_6B), and one each for GZnC (QGznc.iari_7A) and TKW (QTkw.iari_4B) were identified. A total of two stable and co-localized QTLs (QGpc.iari_4B and QTkw.iari_4B) were identified on the 4B chromosome between the flanking region of Xgwm149–AX-94559916. In silico analysis revealed that the key putative candidate genes such as P-loop containing nucleoside triphosphatehydrolase, Nodulin-like protein, NAC domain, Purine permease, Zinc-binding ribosomal protein, Cytochrome P450, Protein phosphatase 2A, Zinc finger CCCH-type, and Kinesin motor domain were located within the identified QTL regions and these putative genes are involved in the regulation of iron homeostasis, zinc transportation, Fe, Zn, and protein remobilization to the developing grain, regulation of grain size and shape, and increased nitrogen use efficiency. The identified novel QTLs, particularly stable and co-localized QTLs are useful for subsequent use in marker-assisted selection (MAS). Full article
(This article belongs to the Special Issue Wheat Genomics, Genetics and Breeding)
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Review

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15 pages, 1619 KiB  
Review
Ensuring Nutritional Security in India through Wheat Biofortification: A Review
by Umesh Kamble, Chandra Nath Mishra, Velu Govindan, Amit Kumar Sharma, Sushma Pawar, Satish Kumar, Gopalareddy Krishnappa, Om Prakash Gupta, Gyanendra Pratap Singh and Gyanendra Singh
Genes 2022, 13(12), 2298; https://doi.org/10.3390/genes13122298 - 6 Dec 2022
Cited by 5 | Viewed by 2693
Abstract
Undernourishment of nutrients, also known as hidden hunger, affects over 2 billion populace globally. Even though stunting among children below five years of age has decreased in India in the last ten years, India is home to roughly thirty percent of the world’s [...] Read more.
Undernourishment of nutrients, also known as hidden hunger, affects over 2 billion populace globally. Even though stunting among children below five years of age has decreased in India in the last ten years, India is home to roughly thirty percent of the world’s population of stunted pre-schoolers. A significant improvement has been witnessed in the targeted development and deployment of biofortified crops; approximately 20 million farm households from developing counties benefit from cultivating and consuming biofortified crops. There is ample scope for including biofortified varieties in the seed chain, ensuring nutritional security. Wheat is a dietary staple in India, typically consumed as wholemeal flour in the form of flatbreads such as chapatti and roti. Wheat contributes to nearly one fifth of global energy requirements and can also provide better amounts of iron (Fe) and zinc (Zn). As a result, biofortified wheat can serve as a medium for delivery of essential micronutrients such as Fe and Zn to end users. This review discusses wheat biofortification components such as Fe and Zn dynamics, its uptake and movement in plants, the genetics of their buildup, and the inclusion of biofortified wheat varieties in the seed multiplication chain concerning India. Full article
(This article belongs to the Special Issue Wheat Genomics, Genetics and Breeding)
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