Special Issue "Application of Molecular Marker Technology in Crop Breeding"

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

Deadline for manuscript submissions: 10 November 2022 | Viewed by 1683

Special Issue Editor

Dr. Dilip R. Panthee
E-Mail Website
Guest Editor
Department of Horticultural Science, North Carolina State University, Raleigh, NC 27608, USA
Interests: breeding for fruit quality; differential gene expression analysis; genomic selection; GWAS; molecular breeding; plant breeding; QTL mapping; resistance breeding; stress tolerance
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Special Issue Information

Dear Colleagues,

The application of molecular markers in crop improvement first started in the 1980s. Initially, it was in the form of hybridization-based molecular markers, which were relatively less popular. As soon as PCR-based molecular markers became available, however, they became widely and easily applicable in several crop plants. Since then, several plant breeding programs have optimized the use of molecular markers associated with various traits, including disease resistance, quality, and abiotic stress tolerance. Still, there are several traits that need to be optimized, and research on that front is ongoing in various parts of the world. With the availability of genome sequences and SNP markers developed from the use of those sequences, high-density molecular linkage maps can be developed, and molecular markers associated with the traits of interest can be identified more precisely. Furthermore, mapping and fine mapping of QTL can be achieved, and eventually, such research can help us to identify the genes associated with the traits of interest. In the proposed Special Issue of Agronomy, we encourage researchers from around the world to publish their groundbreaking work in these areas of QTL mapping and marker analysis in various plant systems in this Special Issue of Agronomy. Papers directly associated with crop plants of economic importance will be given more priority.

Dr. Dilip R. Panthee
Guest Editor

Manuscript Submission Information

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Keywords

  • GWAS
  • linkage analysis
  • molecular marker
  • QTL
  • RNA-seq analysis

Published Papers (2 papers)

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Research

Article
Identification of Low-Light-Resistant Germplasm and Related Loci of Soybean
Agronomy 2022, 12(7), 1483; https://doi.org/10.3390/agronomy12071483 - 21 Jun 2022
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Abstract
Low-light stress will lead to abnormal soybean growth and a subsequent yield reduction. Association mapping is a useful alternative to linkage mapping for the detection of marker–phenotype associations. This study aimed to evaluate low-light-resistant soybean accessions and identify markers associated with low-light resistance. [...] Read more.
Low-light stress will lead to abnormal soybean growth and a subsequent yield reduction. Association mapping is a useful alternative to linkage mapping for the detection of marker–phenotype associations. This study aimed to evaluate low-light-resistant soybean accessions and identify markers associated with low-light resistance. We assessed the plant height, stem diameter, number of bean pods, and cotyledon height of soybean plants under low and normal light conditions. These traits were evaluated in 185 soybean accessions, and the accessions 11HX-020, 11HX-025, 11HX-029, 11HX-064, 11HX-127, 11HX-166, 11HX-183, and 11HX-216 showed stable performance under low-light conditions. These 185 accessions were genotyped with 639 single-nucleotide polymorphism (SNP) markers and 98 simple sequence repeat (SSR) markers. A total of 75 markers—i.e., traits associated with low-light resistance—were identified. These associated markers were distributed on 14 linkage groups (LGs) of soybean, and some markers were associated with two or more traits. According to the results, excellent germplasm material and low-light-resistance related markers can be used for low-light resistance breeding of soybean and will help identify the low-light resistance genes. Full article
(This article belongs to the Special Issue Application of Molecular Marker Technology in Crop Breeding)
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Article
Integrating Genome-Wide Association Study with Transcriptomic Analysis to Predict Candidate Genes Controlling Storage Root Flesh Color in Sweet Potato
Agronomy 2022, 12(5), 991; https://doi.org/10.3390/agronomy12050991 - 20 Apr 2022
Viewed by 624
Abstract
Sweet potato is a hexaploid heterozygote with a complex genetic background, self-pollination infertility, and cross incompatibility, which makes genetic linkage analysis quite difficult. Genome-wide association studies (GWAS) provide a new strategy for gene mapping and cloning in sweet potato. Storage root flesh color [...] Read more.
Sweet potato is a hexaploid heterozygote with a complex genetic background, self-pollination infertility, and cross incompatibility, which makes genetic linkage analysis quite difficult. Genome-wide association studies (GWAS) provide a new strategy for gene mapping and cloning in sweet potato. Storage root flesh color (SRFC) is an important sensory evaluation, which correlates with storage root flesh composition, such as starch, anthocyanin, and carotenoid. We performed GWAS using SRFC data of 300 accessions and 567,828 single nucleotide polymorphism (SNP) markers. Furthermore, we analyzed transcriptome data of different SRFC varieties, and conducted real-time quantitative PCR (qRT-PCR) to measure the expression level of the candidate gene in purple and non-purple fleshed sweet potato genotypes. The results showed that five unique SNPs were significantly (−log10P > 7) associated with SRFC. Based on these trait-associated SNPs, four candidate genes, g55964 (IbF3′H), g17506 (IbBAG2-like), g25206 (IbUGT-73D1-like), and g58377 (IbVQ25-isoform X2) were identified. Expression profiles derived from transcriptome data and qRT-PCR analyses showed that the expression of g55964 in purple-fleshed sweet potato was significantly (p < 0.01) higher than that of non-purple fleshed sweet potato. By combining the GWAS, transcriptomic analysis and qRT-PCR, we inferred that g55964 is the key gene related to purple formation of storage root in sweet potato. Our results lay the foundation for accelerating sweet potato genetic improvement of anthocyanin through marker-assisted selection. Full article
(This article belongs to the Special Issue Application of Molecular Marker Technology in Crop Breeding)
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