Genomics-Assisted Breeding: Strategies, Advances and Challenges

A special issue of Biomolecules (ISSN 2218-273X). This special issue belongs to the section "Molecular Genetics".

Deadline for manuscript submissions: closed (15 March 2022) | Viewed by 12403

Special Issue Editor


E-Mail Website
Guest Editor
College of Agronomy and Biotechnology, Southwest University, Chongqing, China
Interests: crop yield; seed development; genome evolution in polyploids; genomic breeding; multi-omics integration; gene regulatory networks; biological database

Special Issue Information

Dear Colleagues,

With the rapid increase in the world population, crop improvement has become the most effective way to boost global food security. Compared with conventional breeding approaches, marker-assisted selection (MAS) has greatly enhanced the efficiency of plant breeding and crop improvement, due to the switch from phenotype-based toward genotype-based selection. More recently, several novel genomics-assisted breeding (GAB) tools/approaches such as genome-wide association studies (GWAS), genomic selection (GS), de novo domestication, gene or genome editing, etc. have been extensively studied and achieved significant progress in plant science. However, their successful implementation in practical breeding for the improvement of complex traits such as yield and stress tolerance has rarely been explored. We expect that GAB approaches will be more extensively investigated and widely utilized in future plant breeding. Therefore, this Special Issue aims to help readers to understand the roles of GAB in crop improvement. It is dedicated to original research and review articles which cover recent progress in the identification of quantitative trait loci (QTLs), quantitative trait nucleotides (QTNs), and functional markers associated with complex traits in agronomically important crops, and functional characterization of a causative gene. New tools and methodologies and their breeding applications involved in high-throughput phenotyping and genotyping, association and linkage mapping, GS and phenotype prediction, gene and genome editing, de novo domestication, genome design for future crops, artificially synthesized crops, and integrative GAB approaches are also of particular interest.

Prof. Dr. Kun Lu
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. Biomolecules 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 2700 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

  • Genomics
  • Plant breeding
  • Crop improvement
  • Complex trait
  • Genome-wide association studies
  • Genomic selection
  • High-throughput phenotyping

Published Papers (4 papers)

Order results
Result details
Select all
Export citation of selected articles as:

Research

Jump to: Review

17 pages, 5710 KiB  
Article
Fine Mapping and Characterization of a Major Gene Responsible for Chlorophyll Biosynthesis in Brassica napus L.
by Chengke Pang, Wei Zhang, Menlu Peng, Xiaozhen Zhao, Rui Shi, Xu Wu, Feng Chen, Chengming Sun, Xiaodong Wang and Jiefu Zhang
Biomolecules 2022, 12(3), 402; https://doi.org/10.3390/biom12030402 - 4 Mar 2022
Cited by 3 | Viewed by 2136
Abstract
Rapeseed (Brassica napus L.) is mainly used for oil production and industrial purposes. A high photosynthetic efficiency is the premise of a high yield capable of meeting people’s various demands. Chlorophyll-deficient mutants are ideal materials for studying chlorophyll biosynthesis and photosynthesis. In [...] Read more.
Rapeseed (Brassica napus L.) is mainly used for oil production and industrial purposes. A high photosynthetic efficiency is the premise of a high yield capable of meeting people’s various demands. Chlorophyll-deficient mutants are ideal materials for studying chlorophyll biosynthesis and photosynthesis. In a previous study, we obtained the mutant yl1 for leaf yellowing throughout the growth period by ethyl methanesulfonate mutagenesis of B. napus. A genetic analysis showed that the yl1 chlorophyll-deficient phenotype was controlled by one incompletely dominant gene, which was mapped on chromosome A03 by a quantitative trait loci sequencing analysis and designated as BnA03.Chd in this study. We constructed an F2 population containing 5256 individuals to clone BnA03.Chd. Finally, BnA03.Chd was fine-mapped to a 304.7 kb interval of the B. napus ‘ZS11’ genome containing 58 annotated genes. Functional annotation, transcriptome, and sequence variation analyses confirmed that BnaA03g0054400ZS, a homolog of AT5G13630, was the most likely candidate gene. BnaA03g0054400ZS encodes the H subunit of Mg-chelatase. A sequence analysis revealed a single-nucleotide polymorphism (SNP), causing an amino-acid substitution from glutamic acid to lysine (Glu1349Lys). In addition, the molecular marker BnaYL1 was developed based on the SNP of BnA03.Chd, which perfectly cosegregated with the chlorophyll-deficient phenotype in two different F2 populations. Our results provide insight into the molecular mechanism underlying chlorophyll synthesis in B. napus. Full article
(This article belongs to the Special Issue Genomics-Assisted Breeding: Strategies, Advances and Challenges)
Show Figures

Figure 1

17 pages, 1093 KiB  
Article
Quantitative Trait Locus Mapping Combined with RNA Sequencing Reveals the Molecular Basis of Seed Germination in Oilseed Rape
by Kunjiang Yu, Yuqi He, Yuanhong Li, Zhenhua Li, Jiefu Zhang, Xiaodong Wang and Entang Tian
Biomolecules 2021, 11(12), 1780; https://doi.org/10.3390/biom11121780 - 27 Nov 2021
Cited by 3 | Viewed by 1620
Abstract
Rapid and uniform seed germination improves mechanized oilseed rape production in modern agricultural cultivation practices. However, the molecular basis of seed germination is still unclear in Brassica napus. A population of recombined inbred lines of B. napus from a cross between the [...] Read more.
Rapid and uniform seed germination improves mechanized oilseed rape production in modern agricultural cultivation practices. However, the molecular basis of seed germination is still unclear in Brassica napus. A population of recombined inbred lines of B. napus from a cross between the lower germination rate variety ‘APL01’ and the higher germination rate variety ‘Holly’ was used to study the genetics of seed germination using quantitative trait locus (QTL) mapping. A total of five QTLs for germination energy (GE) and six QTLs for germination percentage (GP) were detected across three seed lots, respectively. In addition, six epistatic interactions between the QTLs for GE and nine epistatic interactions between the QTLs for GP were detected. qGE.C3 for GE and qGP.C3 for GP were co-mapped to the 28.5–30.5 cM interval on C3, which was considered to be a novel major QTL regulating seed germination. Transcriptome analysis revealed that the differences in sugar, protein, lipid, amino acid, and DNA metabolism and the TCA cycle, electron transfer, and signal transduction potentially determined the higher germination rate of ‘Holly’ seeds. These results contribute to our knowledge about the molecular basis of seed germination in rapeseed. Full article
(This article belongs to the Special Issue Genomics-Assisted Breeding: Strategies, Advances and Challenges)
Show Figures

Figure 1

Review

Jump to: Research

14 pages, 900 KiB  
Review
Biomolecular Strategies for Vascular Bundle Development to Improve Crop Yield
by Wei Chang, Hongqiao Chen, Guixiang Jiao, Yi Dou, Lin Liu, Cunmin Qu, Jiana Li and Kun Lu
Biomolecules 2022, 12(12), 1772; https://doi.org/10.3390/biom12121772 - 28 Nov 2022
Viewed by 3276
Abstract
The need to produce crops with higher yields is critical due to a growing global population, depletion of agricultural land, and severe climate change. Compared with the “source” and “sink” transport systems that have been studied a lot, the development and utilization of [...] Read more.
The need to produce crops with higher yields is critical due to a growing global population, depletion of agricultural land, and severe climate change. Compared with the “source” and “sink” transport systems that have been studied a lot, the development and utilization of vascular bundles (conducting vessels in plants) are increasingly important. Due to the complexity of the vascular system, its structure, and its delicate and deep position in the plant body, the current research on model plants remains basic knowledge and has not been repeated for crops and applied to field production. In this review, we aim to summarize the current knowledge regarding biomolecular strategies of vascular bundles in transport systems (source-flow-sink), allocation, helping crop architecture establishment, and influence of the external environment. It is expected to help understand how to use sophisticated and advancing genetic engineering technology to improve the vascular system of crops to increase yield. Full article
(This article belongs to the Special Issue Genomics-Assisted Breeding: Strategies, Advances and Challenges)
Show Figures

Figure 1

17 pages, 1548 KiB  
Review
Advances and Challenges for QTL Analysis and GWAS in the Plant-Breeding of High-Yielding: A Focus on Rapeseed
by Shahid Ullah Khan, Sumbul Saeed, Muhammad Hafeez Ullah Khan, Chuchuan Fan, Sunny Ahmar, Osvin Arriagada, Raheel Shahzad, Ferdinando Branca and Freddy Mora-Poblete
Biomolecules 2021, 11(10), 1516; https://doi.org/10.3390/biom11101516 - 15 Oct 2021
Cited by 23 | Viewed by 4668
Abstract
Yield is one of the most important agronomic traits for the breeding of rapeseed (Brassica napus L), but its genetic dissection for the formation of high yield remains enigmatic, given the rapid population growth. In the present review, we review the discovery [...] Read more.
Yield is one of the most important agronomic traits for the breeding of rapeseed (Brassica napus L), but its genetic dissection for the formation of high yield remains enigmatic, given the rapid population growth. In the present review, we review the discovery of major loci underlying important agronomic traits and the recent advancement in the selection of complex traits. Further, we discuss the benchmark summary of high-throughput techniques for the high-resolution genetic breeding of rapeseed. Biparental linkage analysis and association mapping have become powerful strategies to comprehend the genetic architecture of complex agronomic traits in crops. The generation of improved crop varieties, especially rapeseed, is greatly urged to enhance yield productivity. In this sense, the whole-genome sequencing of rapeseed has become achievable to clone and identify quantitative trait loci (QTLs). Moreover, the generation of high-throughput sequencing and genotyping techniques has significantly enhanced the precision of QTL mapping and genome-wide association study (GWAS) methodologies. Furthermore, this study demonstrates the first attempt to identify novel QTLs of yield-related traits, specifically focusing on ovule number per pod (ON). We also highlight the recent breakthrough concerning single-locus-GWAS (SL-GWAS) and multi-locus GWAS (ML-GWAS), which aim to enhance the potential and robust control of GWAS for improved complex traits. Full article
(This article belongs to the Special Issue Genomics-Assisted Breeding: Strategies, Advances and Challenges)
Show Figures

Figure 1

Back to TopTop