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Molecular Genetics, Genomics and Breeding of Cereal Crops

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A special issue of Agronomy (ISSN 2073-4395). This special issue belongs to the section "Crop Breeding and Genetics".

Deadline for manuscript submissions: closed (15 March 2021) | Viewed by 20258

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Special Issue Editors

Dr. Ahmad M. Alqudah

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Guest Editor

Department Genebank, Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany
Interests: agronomy; cereals; crop physiology; plant breeding; plant genetics; genomics; boinformatics

Prof. Dr. Andreas Börner

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Guest Editor

Department Genebank, Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany
Interests: germplasm; seed longevity; genetic integrity; genetic diversity
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

The improvement of crop yield has been a fundamental human goal since cultivation began. Cereal crops, including wheat, rice, corn, barley, oat, rye, millet, and sorghum from the Poaceae family, are considered to be the main source of human dietary calories and animal feeding. While modern cereal breeding continues to select for better yield, further optimization of yield-related traits under various conditions is essential to meet the predicted increases in grain demand. Understanding cereal yield and translating this knowledge in breeding programs is an elusive target for cereal crop breeders.

Many quantitative trait locus/loci (QTL(s)) or markers linked to yield have been identified and incorporated in breeding for crop yield improvement in cereals. The recent advances in next-generation sequencing (NGS) have paved the way to genetically improve the important traits (grain yield and quality, biotic and abiotic stress tolerance, etc.) in cereal crops. The output of QTL, genome-wide association scan (GWAS), and genomic selection (GS) can be implemented in many molecular aspects, e.g., breeding, genetic mapping, candidate gene identification, and gene editing. Interestingly, integrating -omics and genetics will be crucial for crop improvement and molecular analysis.

The knowledge gained from this Special Issue will play a fundamental role in cereal yield improvement. Therefore, we encourage the submission of novel studies addressing QTL, GWAS, GS, transcriptomics, bioinformatics, and genomics aimed to understand and improve yield and related characters in cereal crops.

Dr. Andreas Börner
Dr. Ahmad M. Alqudah
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. Agronomy is an international peer-reviewed open access monthly 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 2600 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

Cereal crops;
Temperate cereals;
Breeding;
Natural variation;
QTL;
GWAS;
Genomic selection;
Genomics;
Complex traits;
Next-generation sequencing;
Candidate genes;

Published Papers (5 papers)

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Research

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17 pages, 2178 KiB

Open AccessEditor’s ChoiceArticle

Genetic Gain for Grain Micronutrients and Their Association with Phenology in Historical Wheat Cultivars Released between 1911 and 2016 in Pakistan

by Muzzafar Shaukat, Mengjing Sun, Mohsin Ali, Tariq Mahmood, Samar Naseer, Saman Maqbool, Shoaib Rehman, Zahid Mahmood, Yuanfeng Hao, Xianchun Xia, Awais Rasheed and Zhonghu He

Agronomy 2021, 11(6), 1247; https://doi.org/10.3390/agronomy11061247 - 19 Jun 2021

Cited by 15 | Viewed by 2819

Abstract

Wheat (Triticum aestivum L.), being a staple food crop, is an important nutritional source providing protein and minerals. It is important to fortify staple cereals such as wheat with essential minerals to overcome the problems associated with malnutrition. The experiment was designed to evaluate the status of 11 micronutrients including grain iron (GFe) and zinc (GZn) in 62 wheat cultivars released between 1911 and 2016 in Pakistan. Field trials were conducted over two years and GFe and GZn were quantified by both inductively coupled plasma optical emission spectroscopy (ICP-OES) and energy-dispersive X-ray fluorescence spectrophotometer (EDXRF). The GZn ranged from 18.4 to 40.8 mg/kg by ED-XRF and 23.7 to 38.8 mg/kg by ICP-OES. Similarly, GFe ranged from 24.8 to 44.1 mg/kg by ICP-OES and 26.8 to 36.6 mg/kg by EDEXR. The coefficient of correlation was higher for GZn (r = 0.90), compared to GFe (r = 0.68). Modern cultivars such as Zincol-16 and AAS-2011 showed higher GFe and GZn along with improved yield components. Old wheat cultivars WL-711, C-518 and Pothowar-70, released before 1970, also exhibited higher values of GFe and GZn; however, their agronomic performance was poor. Multivariate analysis using eleven micronutrients (Fe, Zn, Al, Ca, Cu, K, Mg, Mn, Na, Se and P) along with agronomic traits, and genome-wide SNP markers identified the potential cultivar with improved yield, biofortification and wider genetic diversity. Genetic gain analysis identified a significant increase in grain yield (0.4% year⁻¹), while there was negative gain for GFe (−0.11% year⁻¹) and GZn (−0.15% year⁻¹) over the span of 100 years. The Green Revolution Rht-B1 and Rht-D1 genes had a strong association with plant height and grain yield (GY), while semi-dwarfing alleles had a negative effect on GFe and GZn contents. This study provided a valuable insight into the biofortification status of wheat cultivars deployed historically in Pakistan and is a valuable source to initiate a breeding strategy for simultaneous improvement in wheat phenology and biofortification. Full article

(This article belongs to the Special Issue Molecular Genetics, Genomics and Breeding of Cereal Crops)

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19 pages, 2776 KiB

Open AccessArticle

Genotypic and Phenotypic Characterization of Two Triticum aestivum L.—Dasypyrum villosum Translocations Lines in the Same Wheat Genetic Background

by Baicui Wang, Xiaolan Ma, Xingguo Ye, Yilin Zhou, Youzhi Ma and Zhishan Lin

Agronomy 2021, 11(2), 399; https://doi.org/10.3390/agronomy11020399 - 23 Feb 2021

Cited by 3 | Viewed by 2105

Abstract

A wheat 660K chip was used to genotype two wheat-Dasypyrum villosum 6V#4S.6DL and 6V#2S.6AL translocation lines (A303 and B303) and their common wheat recurrent parent Wan7107. The results showed that these three lines have similar characteristics of base composition except for the translocation chromosomes. The alien translocation chromosomes have fewer homozygous and more heterozygous genotypes with more invalid probes. Distributions of SNPs between the translocation lines and Wan7107 were mainly dense on the regions of 6AS or 6DS as expected, but unexpectedly also on near the telomere of 2BS, and some regions of other wheat chromosomes. Meanwhile, the translocation lines A303 and B303 have 99.44% and 98.81% identical genotypes to Wan7107, respectively. Under the same genetic background, A303 and B303 showed different reactions to Blumeria graminis f. sp. tritici (Bgt) strains of powdery mildew. Both translocation lines have higher grain weight and plant height, and B303 has fewer spikelets compared to Wan7107. These results provide us a new insight into the genomic variation between the backcross generation plant and the recurrent parent, which is valuable information for understanding the relationship between wheat and the 6VS chromosome of D. villosum as well as the application potential of the alien chromosome arms. Full article

(This article belongs to the Special Issue Molecular Genetics, Genomics and Breeding of Cereal Crops)

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21 pages, 1906 KiB

Open AccessArticle

Investigation of Heat-Induced Changes in the Grain Yield and Grains Metabolites, with Molecular Insights on the Candidate Genes in Barley

by Mona F. A. Dawood, Yasser S. Moursi, Ahmed Amro, P. Stephen Baenziger and Ahmed Sallam

Agronomy 2020, 10(11), 1730; https://doi.org/10.3390/agronomy10111730 - 6 Nov 2020

Cited by 28 | Viewed by 2771

Abstract

Heat stress is one of the abiotic stresses that cause a significant reduction in barley yield. Climate change will increase the number of heatwaves, which will result in more deterioration in the agricultural sector. Therefore, understanding the physiological changes that occur in the plant to tolerate heat stress is very important. A collection of 60 Egyptian spring barley genotypes has been tested for heat stress under field conditions. To quantify the changes in yield-related traits and the grain-reserve parameters as indicators for heat tolerance, several traits were scored. The causative genes that regulate the variation of all traits of interest were identified via single-marker analysis using 16,966 single nucleotide polymorphisms (SNP). Heat stress reduced yield-related traits, while some physiological traits (chlorophyll index, soluble carbohydrates, amino acids, and proline contents) increased. The genotypes were classified into four classes, A, B, C, and D, based on a reduction in grain yield per spike (GYPS) of 10%, 20%, 30%, and 40%, respectively. The physiological aspects were extensively studied in each group. The tolerant genotypes (class A) retained high yield-related traits as well as high reserved metabolites relative to the sensitive class D. The single-marker analysis and gene annotations revealed that the most effective markers and genes resided on chromosomes 1H and 4H. One of these markers, S4_250499621, was found to be associated with increased proline content, increased chlorophyll content, and decreased reduction in grain yield per spike and thousand kernel weight. This study is a part of our extended evaluation of this collection under various abiotic stresses at different developmental stages to develop climate-resilient crops. Full article

(This article belongs to the Special Issue Molecular Genetics, Genomics and Breeding of Cereal Crops)

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Review

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14 pages, 1561 KiB

Open AccessReview

Advances in Genomics-Based Breeding of Barley: Molecular Tools and Genomic Databases

by Asad Riaz, Farah Kanwal, Andreas Börner, Klaus Pillen, Fei Dai and Ahmad M. Alqudah

Agronomy 2021, 11(5), 894; https://doi.org/10.3390/agronomy11050894 - 2 May 2021

Cited by 15 | Viewed by 6284

Abstract

Barley is the fourth most important cereal crop and has been domesticated and cultivated for more than 10,000 years. Breeding climate-smart and stress-tolerant cultivars is considered the most suitable way to accelerate barley improvement. However, the conventional breeding framework needs to be changed to facilitate genomics-based breeding of barley. The continuous progress in genomics has opened up new avenues and tools that are promising for making barley breeding more precise and efficient. For instance, reference genome assemblies in combination with germplasm sequencing to delineate breeding have led to the development of more efficient barley cultivars. Genetic analysis, such as QTL mapping and GWAS studies using sequencing approaches, have led to the identification of molecular markers, genomic regions and novel genes associated with the agronomic traits of barley. Furthermore, SNP marker technologies and haplotype-based GWAS have become the most applied methods for supporting molecular breeding in barley. The genetic information is also used for high-efficiency gene editing by means of CRISPR-Cas9 technology, the best example of which is the cv. Golden Promise. In this review, we summarize the genomic databases that have been developed for barley and explain how the genetic resources of the reference genome, the available state-of-the-art bioinformatics tools, and the most recent assembly of a barley pan-genome will boost the genomics-based breeding for barley improvement. Full article

(This article belongs to the Special Issue Molecular Genetics, Genomics and Breeding of Cereal Crops)

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18 pages, 452 KiB

Open AccessReview

Advances in Understanding the Molecular Mechanisms and Potential Genetic Improvement for Nitrogen Use Efficiency in Barley

by Sakura D. Karunarathne, Yong Han, Xiao-Qi Zhang and Chengdao Li

Agronomy 2020, 10(5), 662; https://doi.org/10.3390/agronomy10050662 - 8 May 2020

Cited by 16 | Viewed by 5072

Abstract

Nitrogen (N) fertilization plays an important role in crop production; however, excessive and inefficient use of N fertilizer is a global issue that incurs high production costs, pollutes the environment and increases the emission of greenhouse gases. To overcome these negative consequences, improving nitrogen use efficiency (NUE) would be a key factor for profitable crop production either by increasing yield or reducing fertilizer cost. In contrast to soil and crop management practices, understanding the molecular mechanisms in NUE and developing new varieties with improved NUE is more environmentally and economically friendly. In this review, we highlight the recent progress in understanding and improving nitrogen use efficiency in barley, with perspectives on the impact of N on plant morphology and agronomic performance, NUE and its components such as N uptake and utilization, QTLs and candidate genes controlling NUE, and new strategies for NUE improvement. Full article

(This article belongs to the Special Issue Molecular Genetics, Genomics and Breeding of Cereal Crops)

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