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Agronomy
Special Issues
Genetic and Genomic Studies of Important Traits in Cereal Crops
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Genetic and Genomic Studies of Important Traits in Cereal Crops

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

Deadline for manuscript submissions: closed (31 December 2023) | Viewed by 5418

Special Issue Editors

Prof. Dr. Shuyu Liu

E-Mail Website
Guest Editor
Texas A&M AgriLife Research Center, 6500 Amarillo Blvd. West, Amarillo, TX 79106, USA
Interests: wheat breeding; genetics and genomics; gene/QTL mapping; marker-/genomic-assisted selection; genomic prediction; association analyses
Dr. Shisheng Chen

E-Mail Website
Guest Editor
Institute of Advanced Agricultural Sciences, Peking University, Weifang, China
Interests: identification and characterization of disease resistance genes in wheat; mapping, cloning, and functional analysis of R genes; multi-omics approaches to understanding the molecular bases of disease resistance; molecular-marker-assisted breeding for enhancing disease resistance
Special Issues, Collections and Topics in MDPI journals
Prof. Dr. Fa Cui

E-Mail Website
Guest Editor
Key Laboratory of Molecular Module-Based Breeding of High Yield and Abiotic Resistant Plants in Universities of Shandong, School of Agriculture, Ludong University, Yantai 264025, China
Interests: wheat molecular breeding; quantitative genetics; yield-related gene cloning; wheat genomics; genetic improvement of yield in wheat
Prof. Dr. Cheng Liu

E-Mail Website
Guest Editor
Crop Research Institute, Shandong Academy of Agriculture Sciences, 202 Gongyebei Road, Licheng District, Jinan, China
Interests: wheat breeding; wheat and barley genetics and genomics; gene/QTL mapping; wheat wild hybridization
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

The production and end-use quality of cereal food crops require further improvement in order to meet the demands of the growing population worldwide. The technological advancements in genetics and genomics and related data analyses have led to great improvements in the last decade. Single-nucleotide polymorphisms (SNPs) from various platforms including DNA genotyping-by-sequencing, skimseq, whole-genome sequencing, pan genomes, RNA sequencing, exome capture, and their related data analyses have advanced our knowledge in their applications in practical breeding. The goal of this Special Issue is to summarize some of the progress in genomic-assisted breeding for germplasm and cultivar development. We are soliciting papers describing advances in knowledge and progress in the application of these techniques, and how they can be used to improve crop production, resistance, and end-use quality through increasing the resilience of germplasm and cultivars.

Prof. Dr. Shuyu Liu
Dr. Shisheng Chen
Prof. Dr. Fa Cui
Prof. Dr. Cheng Liu
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 crop
  • resilience
  • yield
  • QTL mapping
  • map-based cloning
  • genomic-assisted breeding
  • DNA sequencing
  • exome capture
  • genomic prediction

Published Papers (4 papers)

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Research

12 pages, 1196 KiB  
Article
Marker-Trait Associations of Agronomic Traits in Barley (Hordeum vulgare L.) under Semi-Arid Conditions
by Salem Marzougui and Mongi Ben Younes
Agronomy 2023, 13(11), 2804; https://doi.org/10.3390/agronomy13112804 - 13 Nov 2023
Viewed by 802
Abstract
Heading date, plant height, and spike-related phenotypes are key traits that affect the yield potential and adaptation of barley to Mediterranean environments. These traits are controlled by a complex network of genes as well as environmental effects. Marker-trait associations (MTAs) were performed using [...] Read more.
Heading date, plant height, and spike-related phenotypes are key traits that affect the yield potential and adaptation of barley to Mediterranean environments. These traits are controlled by a complex network of genes as well as environmental effects. Marker-trait associations (MTAs) were performed using a set of 361 barley genotypes, evaluated phenotypically for three years under semi-arid conditions. In total, 24 MTAs were detected using the recently developed GWAS method (BLINK) at –log p ≥ 5. These included one MTA with awn length (Awl) on chromosome 2H; twelve MTAs with heading date (HD) distributed over all chromosomes except 4H; three MTAs with grains per spike (GPS) on chromosomes 1H, 2H, and 6H; six MTAs were detected for plant height (PH) on 2H (2), 3H, 4H, 6H, and 7H; and two MTAs with spike length (SL) on 3H and 7H. The results showed novel and known associations between specific SNP markers and heading date, plant height, and spike-related traits, suggesting that these markers can be used in breeding programs to improve these traits in barley. This study provides valuable information for breeders and geneticists working to develop new barley varieties that are better adapted to semi-arid climates and have improved yield and quality characteristics. Full article
(This article belongs to the Special Issue Genetic and Genomic Studies of Important Traits in Cereal Crops)
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19 pages, 791 KiB  
Article
Mapping QTL for Yield and Its Component Traits Using Wheat (Triticum aestivum L.) RIL Mapping Population from TAM 113 × Gallagher
by Mustafa Cerit, Zhen Wang, Mehmet Dogan, Shuhao Yu, Jorge L. Valenzuela-Antelo, Chenggen Chu, Shichen Wang, Qingwu Xue, Amir M. H. Ibrahim, Jackie C. Rudd, Richard Metz, Charles D. Johnson and Shuyu Liu
Agronomy 2023, 13(9), 2402; https://doi.org/10.3390/agronomy13092402 - 17 Sep 2023
Viewed by 1465
Abstract
Understanding genetic architectures of yield and yield-related traits of wheat (Triticum aestivum L.) grown under dryland or irrigated conditions is pivotal for developing modern high-yielding germplasm and cultivars. The objectives of this study were to detect quantitative trait loci (QTL) linked to [...] Read more.
Understanding genetic architectures of yield and yield-related traits of wheat (Triticum aestivum L.) grown under dryland or irrigated conditions is pivotal for developing modern high-yielding germplasm and cultivars. The objectives of this study were to detect quantitative trait loci (QTL) linked to yield and yield components using a mapping population derived from ‘TAM 113’/‘Gallagher’, including 191 recombinant inbred lines (RILs). The population was grown in McGregor, College Station, and Bushland, Texas, for three consecutive years from 2019 to 2021. A high-density genetic map covering all 21 chromosomes was constructed using a set of 8,075 single nucleotide polymorphisms (SNPs) obtained using genotyping-by-sequencing (GBS). A total of 147 QTLs for 16 yield-related traits were identified, which included 16 QTLs consistently detected in multiple experiments and 8 QTLs that showed pleiotropic effects. Of them, five pleiotropic QTLs overlapped with the consistent QTL. They increased grain yield (YLD) up to 37.64 g m−2, thousand kernel weight (TKW) up to 1.33 g, harvest (HI) up to 0.97%, kernel length up to 0.08 mm, and kernel width up to 0.04 mm with Gallagher alleles and increased YLD up to 22.21 g m−2, kernels spike−1 up to 1.77, TKW up to 1.14 g, and HI up to 3.72% with TAM 113 alleles. One major and consistent QTL on chromosome 2D at 34.4 Mbp overlapped with the major photoperiod gene Ppd-D1 and was affected by multiple traits, including kernel diameter (DIAM), TKW, kernel hardness index (KHI), heading date (HD), and plant height (PH). Another QTL cluster region on 7D between 52 and 66 Mbp, encompassing one consistent and three pleiotropic QTLs. One of the pleiotropic QTLs at 52 Mbp increased YLD up to 24.16 g m−2, HI up to 1%, and DIAM up to 0.03 mm. This study dissected genetic loci associated with yield and yield-related traits, providing valuable information on wheat improvement using marker-assisted selection (MAS). Full article
(This article belongs to the Special Issue Genetic and Genomic Studies of Important Traits in Cereal Crops)
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11 pages, 706 KiB  
Article
Breeding Dual-Purpose Maize: Grain Production and Biofuel Conversion of the Stover
by Noemi Gesteiro, Ana Butrón, Rogelio Santiago, Leonardo D. Gomez, Ana López-Malvar, Lorena Álvarez-Iglesias, Pedro Revilla and Rosa Ana Malvar
Agronomy 2023, 13(5), 1352; https://doi.org/10.3390/agronomy13051352 - 11 May 2023
Cited by 2 | Viewed by 1340
Abstract
The improvement of maize double cropping has become increasingly important in recent years. In order to establish breeding programs for sustainable maize production, the goals of the research were (i) to understand the correlations between grain and stover yield and saccharification efficiency, and [...] Read more.
The improvement of maize double cropping has become increasingly important in recent years. In order to establish breeding programs for sustainable maize production, the goals of the research were (i) to understand the correlations between grain and stover yield and saccharification efficiency, and (ii) to identify QTL and metabolic pathways to design of breeding programs in a double exploitation approach. We carried out a genome-wide association study (GWAS) and a metabolic pathway analysis using a panel of highly diverse maize inbreds. As results, we have obtained that the regulation of energetic and developmental pathways have been pointed out as key pathways related to stover quantity and utilization, while no specific pathways could be identified in relation to grain yield. However, due to the moderate high heritability of yields and their positive correlation a phenotypic selection approach would be adequate for the improvement of both yields, while for saccharification efficiency improvement upcoming genomic selection models are more advisable. Overall, breeding strategies that manage the dual use of maize are viable and will contribute to a more sustainable maize crop in the near future. Full article
(This article belongs to the Special Issue Genetic and Genomic Studies of Important Traits in Cereal Crops)
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18 pages, 2952 KiB  
Article
Identification and Cloning of a Putative Male Fertility Gene Encoding an Oxidosqualene Cyclase in Qingke
by Dian Lin, Zhibin Xu, Bo Feng, Qiang Zhou, Xiaoli Fan and Tao Wang
Agronomy 2023, 13(5), 1292; https://doi.org/10.3390/agronomy13051292 - 30 Apr 2023
Cited by 1 | Viewed by 1314
Abstract
Anther development is crucial for controlling crop fertility. To elucidate the underlying mechanisms of reproductive development of highland barley (called Qingke in Chinese), two main Qingke cultivars, Zangqing 2000 and Ximala 22, were utilized. Transcriptome analysis showed that lipid, sugar and phenylpropane metabolisms [...] Read more.
Anther development is crucial for controlling crop fertility. To elucidate the underlying mechanisms of reproductive development of highland barley (called Qingke in Chinese), two main Qingke cultivars, Zangqing 2000 and Ximala 22, were utilized. Transcriptome analysis showed that lipid, sugar and phenylpropane metabolisms might be the major pathways associated with Qingke male fertility by analyzing the possible common DEGs before anther maturation in both varieties. Additionally, 26 genes related to crop genic male sterility were screened to identify homologous genes for Qingke male sterile lines. Among them, HORVU.MOREX.r3.7HG0634780 (HvtOSC12), an oxidosqualene cyclase, was highlighted as a candidate gene for affecting Qingke male fertility, as it is highly and especially expressed before Qingke anther maturation. Furthermore, HvtOSC12 (including promoter sequence) was cloned by homology-based cloning. The further bioinformatic analysis deduced that MYBs might be one of the transcription factors affecting expression of HvtOSC12 by responding to environmental changes. These results might lay a foundation for the potential applications for the creation of environment-sensitive genic male sterility in Qingke. Full article
(This article belongs to the Special Issue Genetic and Genomic Studies of Important Traits in Cereal Crops)
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