Submit to IJMS Review for IJMS Propose a Special Issue

Journal Menu

Journal Browser

Genetics and Genomics-Based Crop Improvement and Breeding

Print Special Issue Flyer
Special Issue Editors
Special Issue Information
Keywords
Published Papers

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Plant Sciences".

Deadline for manuscript submissions: closed (30 May 2023) | Viewed by 19042

Share This Special Issue

Special Issue Editor

Prof. Dr. Jian Ma

E-Mail Website
Guest Editor

State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu 611130, China
Interests: wheat molecular genetics and genomics
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

In the past decades, although plant breeding has greatly improved the performance of crops including wheat and its related species, maize, oat, rye, rice, barley, millet, and sorghum steadily, the growing food demand in the world due to the increasing of population and decreasing of available land requires these cereal crops both more productive and resistant to harsher environmental conditions as a result of climate change.

The development of Next Generation Sequencing (NGS) has greatly improved the course of science research. Researchers are facing an unprecedented opportunity to identify genes controlling complex phenotypes and understand how the genes fulfill functions through the interaction between genes and environmental factors. This provides a new approach for breeding programs in cereals that can significantly reduce the cost and time needed by traditional breeding or domestication approaches. However, we should note that most of breeding programs still mainly depend on conventional breeding selection performed in repeated and time-consuming field work.

Therefore, it is rather essential to make full use of the advancements on NGS of cereal crops and high-throughput phenotyping and genotyping platforms to genetically identify, evaluate, excavate, characterize more germplasm resources and loci/genes toward at crop improvement.

In this Research Topic aiming at promoting improvent of cereal crops, we are going to collect Original Research, Review, Methods, Mini Review, Perspective, and Opinion articles on, but not limited to, the following areas:

Potential areas in this Research Topic include, but are not limited to:
Identification, evaluation, and characterization of various germplasm;
Identification and breeding utilization of favorable alleles which have not been fully explored;
Genetic mapping, fine mapping, genome wide association analysis of loci/genes for important traits;
Development and breeding utilization of molecular markers tightly linked to important traits;
Structural and functional genomics in crops, proteomics and metabolic profiling, and field evaluation of crops containing particular traits.

Prof. Dr. Jian Ma
Guest Editor

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. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. There is an Article Processing Charge (APC) for publication in this open access journal. For details about the APC please see here. 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

crop
germplasm
genecits
genomics
breeding

Published Papers (9 papers)

Download All Papers

Order results

Result details

Show export options Show export options

Select all

Export citation of selected articles as:

Research

Jump to: Review

16 pages, 1428 KiB

Open AccessArticle

QTL Mapping of Agronomic and Physiological Traits at the Seedling and Maturity Stages under Different Nitrogen Treatments in Barley

by Zhaoyong Zeng, Shiyun Song, Jian Ma, Deyi Hu, Yinggang Xu, Yao Hou, Chengjun He, Xiaoyan Tang, Ting Lan, Jian Zeng, Xuesong Gao and Guangdeng Chen

Int. J. Mol. Sci. 2023, 24(10), 8736; https://doi.org/10.3390/ijms24108736 - 13 May 2023

Cited by 2 | Viewed by 1689

Abstract

Nitrogen (N) stress seriously constrains barley (Hordeum vulgare L.) production globally by influencing its growth and development. In this study, we used a recombinant inbred line (RIL) population of 121 crosses between the variety Baudin and the wild barley accession CN4027 to detect QTL for 27 traits at the seedling stage in hydroponic culture trials and 12 traits at the maturity stage in field trials both under two N treatments, aiming to uncover favorable alleles for N tolerance in wild barley. In total, eight stable QTL and seven QTL clusters were detected. Among them, the stable QTL Qtgw.sau-2H located in a 0.46 cM interval on the chromosome arm 2HL was a novel QTL specific for low N. Notably, Clusters C4 and C7 contained QTL for traits at both the seedling and maturity stages. In addition, four stable QTLs in Cluster C4 were identified. Furthermore, a gene (HORVU2Hr1G080990.1) related to grain protein in the interval of Qtgw.sau-2H was predicted. Correlation analysis and QTL mapping showed that different N treatments significantly affected agronomic and physiological traits at the seedling and maturity stages. These results provide valuable information for understanding N tolerance as well as breeding and utilizing the loci of interest in barley. Full article

(This article belongs to the Special Issue Genetics and Genomics-Based Crop Improvement and Breeding)

► Show Figures

Figure 1

23 pages, 10466 KiB

Open AccessArticle

Utilizing Genomics to Characterize the Common Oat Gene Pool—The Story of More Than a Century of Polish Breeding

by Aneta Koroluk, Sylwia Sowa, Maja Boczkowska and Edyta Paczos-Grzęda

Int. J. Mol. Sci. 2023, 24(7), 6547; https://doi.org/10.3390/ijms24076547 - 31 Mar 2023

Cited by 1 | Viewed by 1532

Abstract

This study was undertaken to investigate the diversity and population structure of 487 oat accessions, including breeding lines from the ongoing programs of the three largest Polish breeding companies, along with modern and historical Polish and foreign cultivars. The analysis was based on 7411 DArTseq-derived SNPs distributed among three sub-genomes (A, C, and D). The heterogeneity of the studied material was very low, as only cultivars and advanced breeding lines were examined. Principal component analysis (PCA), principal coordinate analysis (PCoA), and cluster and STRUCTURE analyses found congruent results, which show that most of the examined cultivars and materials from Polish breeding programs formed major gene pools, that only some accessions derived from Strzelce Plant Breeding, and that foreign cultivars were outside of the main group. During the 120 year oat breeding process, only 67 alleles from the old gene pool were lost and replaced by 67 new alleles. The obtained results indicate that no erosion of genetic diversity was observed within the Polish native oat gene pool. Moreover, current oat breeding programs have introduced 673 new alleles into the gene pool relative to historical cultivars. The analysis also showed that most of the changes in relation to historical cultivars occurred within the A sub-genome with emphasis on chromosome 6A. The targeted changes were the rarest in the C sub-genome. This study showed that Polish oat breeding based mainly on traditional breeding methods—although focused on improving traits typical to this crop, i.e., enhancing the grain yield and quality and improving adaptability—did not significantly narrow the oat gene pool and in fact produced cultivars that are not only competitive in the European market but are also reservoirs of new alleles that were not found in the analyzed foreign materials. Full article

(This article belongs to the Special Issue Genetics and Genomics-Based Crop Improvement and Breeding)

► Show Figures

Figure 1

14 pages, 2881 KiB

Open AccessArticle

BocODD1 and BocODD2 Regulate the Biosynthesis of Progoitrin Glucosinolate in Chinese Kale

by Shuanghua Wu, Ting Zhang, Yudan Wang, Muxi Chen, Jianguo Yang, Fei Li, Ying Deng, Zhangsheng Zhu, Jianjun Lei, Guoju Chen, Bihao Cao and Changming Chen

Int. J. Mol. Sci. 2022, 23(23), 14781; https://doi.org/10.3390/ijms232314781 - 26 Nov 2022

Cited by 1 | Viewed by 1484

Abstract

Progoitrin (2-hydroxy-3-butenyl glucosinolate, PRO) is the main source of bitterness of Brassica plants. Research on the biosynthesis of PRO glucosinolate can aid the understanding of the nutritional value in Brassica plants. In this study, four ODD genes likely involved in PRO biosynthesis were cloned from Chinese kale. These four genes, designated as BocODD1–4, shared 75–82% similarities with the ODD sequence of Arabidopsis. The sequences of these four BocODDs were analyzed, and BocODD1 and BocODD2 were chosen for further study. The gene BocODD1,2 showed the highest expression levels in the roots, followed by the leaves, flowers, and stems, which is in accordance with the trend of the PRO content in the same tissues. Both the expression levels of BocODD1,2 and the content of PRO were significantly induced by high- and low-temperature treatments. The function of BocODDs involved in PRO biosynthesis was identified. Compared with the wild type, the content of PRO was increased twofold in the over-expressing BocODD1 or BocODD2 plants. Meanwhile, the content of PRO was decreased in the BocODD1 or BocODD2 RNAi lines more than twofold compared to the wildtype plants. These results suggested that BocODD1 and BocODD2 may play important roles in the biosynthesis of PRO glucosinolate in Chinese kale. Full article

(This article belongs to the Special Issue Genetics and Genomics-Based Crop Improvement and Breeding)

► Show Figures

Figure 1

16 pages, 2270 KiB

Open AccessArticle

Effects of Exogenous α-Naphthaleneacetic Acid and 24-Epibrassinolide on Fruit Size and Assimilate Metabolism-Related Sugars and Enzyme Activities in Giant Pumpkin

by Chen Chen, Xuan-Min Wu, Liu Pan, Ya-Ting Yang, Hai-Bo Dai, Bing Hua, Min-Min Miao and Zhi-Ping Zhang

Int. J. Mol. Sci. 2022, 23(21), 13157; https://doi.org/10.3390/ijms232113157 (registering DOI) - 29 Oct 2022

Cited by 9 | Viewed by 1789

Abstract

Size is the most important quality attribute of giant pumpkin fruit. Different concentrations and application frequencies of α-naphthaleneacetic acid (NAA) and 24-epibrassinolide (EBR) were sprayed on the leaves and fruits of giant pumpkin at different growth stages to determine their effects and the mechanism responsible for fruit size increase. NAA+EBR application improved source strength, and further analysis indicated that NAA+EBR markedly boosted net photosynthetic rate (Pn), stomatal conductance (Gs), transpiration rate (Tr) and the expression level and activity of galactitol synthetase (GolS), raffinose synthetase (RS), and stachyose synthetase (STS), resulting in an increase in the synthesis of photoassimilate, especially stachyose. Concomitantly, NAA+EBR spray increased stachyose and sucrose contents throughout pumpkin fruit growth and the concentrations of glucose and fructose at 0 and 20 days post-anthesis (DPA) in peduncle phloem sap, implying that such treatment improved the efficiency of assimilate transport from the peduncle to the fruit. Furthermore, it improved the expression and activity of alkaline α-galactosidase (AGA), facilitating assimilate unloading, providing carbon skeletons and energy for fruit growth, and increasing fruit weight by more than 44.1%. Therefore, exogenous NAA and EBR increased source capacity, transportation efficiency, and sink strength, overall promoting the synthesis and distribution of photoassimilate, ultimately increasing fruit size. Full article

(This article belongs to the Special Issue Genetics and Genomics-Based Crop Improvement and Breeding)

► Show Figures

Figure 1

15 pages, 3177 KiB

Open AccessArticle

The WRKY Transcription Factor OsWRKY54 Is Involved in Salt Tolerance in Rice

by Jingjing Huang, Fuhang Liu, Dong Chao, Boning Xin, Kui Liu, Shuling Cao, Xingxiang Chen, Liyun Peng, Baolei Zhang, Shan Fu and Jixing Xia

Int. J. Mol. Sci. 2022, 23(19), 11999; https://doi.org/10.3390/ijms231911999 - 9 Oct 2022

Cited by 20 | Viewed by 3042

Abstract

Salt stress is a critical limiting factor for rice growth and production. Although numerous salt-tolerant genes have been identified, the mechanism underlying salt stress tolerance in rice remains unclear. This study reports the need for an uncharacterized WRKY transcription factor OsWRKY54 for rice salt-tolerance. Salt stress resulted in a rapid induction of OsWRKY54 expression in roots. Immunostaining analysis showed that it was mainly expressed in the stele. The loss of OsWRKY54 resulted in greater Na accumulation in shoots and enhanced sensitivity of rice plants to salt stress. The real-time quantitative PCR (qRT-PCR) and transcriptome analysis revealed that OsWRKY54 regulated the expression of some essential genes related to salt tolerance, such as OsNHX4 and OsHKT1;5. Furthermore, OsWRKY54 was found to regulate OsHKT1;5 expression by directly binding to the W-box motif in its promoter. Thus, these results indicated that OsWRKY54 was a critical regulatory factor in salt tolerance in rice. Full article

(This article belongs to the Special Issue Genetics and Genomics-Based Crop Improvement and Breeding)

► Show Figures

Figure 1

13 pages, 5509 KiB

Open AccessArticle

Effect of Exogenous Glycine Betaine on the Germination of Tomato Seeds under Cold Stress

by Yingying Zhang, Taoyu Dai, Yahui Liu, Jinyan Wang, Quanhua Wang and Weimin Zhu

Int. J. Mol. Sci. 2022, 23(18), 10474; https://doi.org/10.3390/ijms231810474 - 9 Sep 2022

Cited by 10 | Viewed by 2316

Abstract

Cold stress is known to influence tomato growth, development, and yield. In this study, we analyzed the germination of tomato seeds treated with exogenous glycine betaine (GB) at a low temperature (14 °C). The results showed that cold stress inhibited tomato seed germination, and pretreatment with exogenous GB reduced this inhibition and enhanced the germination rate (GR), germination index (GI), and viability of tomato seeds at low temperatures. Analysis of gene expression and metabolism revealed that GB positively regulated endogenous hormone gibberellin (GA) content and negatively regulated abscisic acid (ABA) content, while GB reduced the starch content in the seeds by up-regulating the amylase gene expression. Gene expression analysis showed that the key genes (SlSOD, SlPOD, and SlchlAPX) involved in reactive oxygen species (ROS) scavenging systems were up-regulated in GB-pretreated tomato seeds compared with the control. At the same time, levels of malondialdehyde and hydrogen peroxide were significantly lower, while the proline content and peroxidase (POD), superoxide dismutase (SOD), and catalase (CAT) levels were elevated compared with those in the control. These results demonstrate that exogenous GB as a positive regulator effectively alleviated the inhibition of tomato seed germination under cold stress by different signal pathways. Full article

(This article belongs to the Special Issue Genetics and Genomics-Based Crop Improvement and Breeding)

► Show Figures

Figure 1

16 pages, 2724 KiB

Open AccessArticle

Cytogenetic and Molecular Marker Analyses of a Novel Wheat–Psathyrostachys huashanica 7Ns Disomic Addition Line with Powdery Mildew Resistance

by Binwen Tan, Miaomiao Wang, Li Cai, Sanyue Li, Wei Zhu, Lili Xu, Yi Wang, Jian Zeng, Xing Fan, Lina Sha, Dandan Wu, Yiran Cheng, Haiqin Zhang, Guoyue Chen, Yonghong Zhou and Houyang Kang

Int. J. Mol. Sci. 2022, 23(18), 10285; https://doi.org/10.3390/ijms231810285 - 7 Sep 2022

Cited by 2 | Viewed by 1638

Abstract

Powdery mildew caused by Blumeria graminis f. sp. tritici is a devastating disease that reduces wheat yield and quality worldwide. The exploration and utilization of new resistance genes from wild wheat relatives is the most effective strategy against this disease. Psathyrostachys huashanica Keng f. ex P. C. Kuo (2n = 2x = 14, NsNs) is an important tertiary gene donor with multiple valuable traits for wheat genetic improvement, especially disease resistance. In this study, we developed and identified a new wheat—P. huashanica disomic addition line, 18-1-5—derived from a cross between P. huashanica and common wheat lines Chinese Spring and CSph2b. Sequential genomic and multicolor fluorescence in situ hybridization analyses revealed that 18-1-5 harbored 21 pairs of wheat chromosomes plus a pair of alien Ns chromosomes. Non-denaturing fluorescence in situ hybridization and molecular marker analyses further demonstrated that the alien chromosomes were derived from chromosome 7Ns of P. huashanica. The assessment of powdery mildew response revealed that line 18-1-5 was highly resistant at the adult stage to powdery mildew pathogens prevalent in China. The evaluation of agronomic traits indicated that 18-1-5 had a significantly reduced plant height and an increased kernel length compared with its wheat parents. Using genotyping-by-sequencing technology, we developed 118 PCR-based markers specifically for chromosome 7Ns of P. huashanica and found that 26 of these markers could be used to distinguish the genomes of P. huashanica and other wheat-related species. Line 18-1-5 can therefore serve as a promising bridging parent for wheat disease resistance breeding. These markers should be conducive for the rapid, precise detection of P. huashanica chromosomes and chromosomal segments carrying Pm resistance gene(s) during marker-assisted breeding and for the investigation of genetic differences and phylogenetic relationships among diverse Ns genomes and other closely related ones. Full article

(This article belongs to the Special Issue Genetics and Genomics-Based Crop Improvement and Breeding)

► Show Figures

Figure 1

25 pages, 6255 KiB

Open AccessArticle

Tracking Changes in the Spring Barley Gene Pool in Poland during 120 Years of Breeding

by Joanna Dziurdziak, Wiesław Podyma, Henryk Bujak and Maja Boczkowska

Int. J. Mol. Sci. 2022, 23(9), 4553; https://doi.org/10.3390/ijms23094553 - 20 Apr 2022

Cited by 5 | Viewed by 1984

Abstract

This study was undertaken to investigate the diversity and population structure of 83 spring barley (Hordeum vulgare L.) cultivars, which corresponded to 120 years of this crop’s breeding in Poland. The analysis was based on 11,655 DArTseq-derived SNPs evenly distributed across seven barley chromosomes. Five groups were assigned in the studied cultivars according to the period of their breeding. A decrease in observed heterozygosity within the groups was noted along with the progress in breeding, with a simultaneous increase in the inbreeding coefficient value. As a result of breeding, some of the unique allelic variation present in old cultivars was lost, but crosses with foreign materials also provided new alleles to the barley gene pool. It is important to mention that the above changes affected different chromosomes to varying degrees. The internal variability of the cultivars ranged from 0.011 to 0.236. Internal uniformity was lowest among the oldest cultivars, although some highly homogeneous ones were found among them. This is probably an effect of genetic drift or selection during their multiplications and regenerations in the period from breeding to the time of analysis. The population genetic structure of the studied group of cultivars appears to be quite complex. It was shown that their genetic makeup consists of as many as eleven distinct gene pools. The analysis also showed traces of directed selection on chromosomes 3H and 5H. Detailed data analysis confirmed the presence of duplicates for 11 cultivars. The performed research will allow both improvement of the management of barley genetic resources in the gene bank and the reuse of this rich and forgotten variability in breeding programs and research. Full article

(This article belongs to the Special Issue Genetics and Genomics-Based Crop Improvement and Breeding)

► Show Figures

Figure 1

Review

Jump to: Research

20 pages, 2301 KiB

Open AccessReview

Genetic Localization and Homologous Genes Mining for Barley Grain Size

by Yi Hong, Mengna Zhang and Rugen Xu

Int. J. Mol. Sci. 2023, 24(5), 4932; https://doi.org/10.3390/ijms24054932 - 3 Mar 2023

Cited by 3 | Viewed by 2089

Abstract

Grain size is an important agronomic trait determining barley yield and quality. An increasing number of QTLs (quantitative trait loci) for grain size have been reported due to the improvement in genome sequencing and mapping. Elucidating the molecular mechanisms underpinning barley grain size is vital for producing elite cultivars and accelerating breeding processes. In this review, we summarize the achievements in the molecular mapping of barley grain size over the past two decades, highlighting the results of QTL linkage analysis and genome-wide association studies. We discuss the QTL hotspots and predict candidate genes in detail. Moreover, reported homologs that determine the seed size clustered into several signaling pathways in model plants are also listed, providing the theoretical basis for mining genetic resources and regulatory networks of barley grain size. Full article

(This article belongs to the Special Issue Genetics and Genomics-Based Crop Improvement and Breeding)

► Show Figures

Journal Menu

Journal Browser

Genetics and Genomics-Based Crop Improvement and Breeding

Share This Special Issue

Special Issue Editor

Special Issue Information

Keywords

Published Papers (9 papers)

Research

Review

Further Information

Guidelines

MDPI Initiatives

Follow MDPI