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Agronomy
Special Issues
Molecular Marker Assisted Crop Breeding
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Molecular Marker Assisted 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: closed (10 June 2022) | Viewed by 9608

Special Issue Editor

Dr. Bo-Keun Ha

E-Mail Website
Guest Editor
Department of Applied Plant Science, Chonnam National University, Gwangju 61186, Republic of Korea
Interests: soybean; cowpea; QTL mapping; GWAS; MAS
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues, 

Molecular marker-assisted breeding has allowed breeders to increase crop production dramatically over the last 30 years. Marker-assisted selection (MAS) shortens the breeding period as well as reducing costs related to developing customized new varieties with superior traits (disease resistance, salt resistance, high quality, high yield, etc.). The availability of the genome sequence for important crop species has now made it easy to find millions of molecular markers which can be used for the genetic dissection of agronomic traits and crop breeding. However, it is still necessary to develop molecular markers that are easily and quickly detected and highly reproducible so that they can be applied to actual breeding programs.

This Special Issue of Agronomy will focus on recent advances in molecular marker-assisted crop breeding. We would like to invite research articles or reviews that are related to the identification of molecular markers linked to quantitative trait loci (QTLs)/genes through various genomic tools, including bi-parental QTL approaches, genome-wide association studies (GWAS), site-directed mutagenesis, etc., and their application for MAS for the development of new cultivars with superior traits in crops.

Dr. Bo-Keun Ha
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. 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

  • crop breeding
  • molecular marker
  • marker-assisted selection (MAS)
  • quantitative trait locus (QTL)
  • genome-wide association study (GWAS)
  • mutagenesis

Published Papers (4 papers)

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Research

15 pages, 2282 KiB  
Article
Genome-Wide Association Study of Leaf Chlorophyll Content Using High-Density SNP Array in Peanuts (Arachis hypogaea L.)
by Kunyan Zou, Ki-Seung Kim, Dongwoo Kang, Min-Cheol Kim, Jungmin Ha, Jung-Kyung Moon and Tae-Hwan Jun
Agronomy 2022, 12(1), 152; https://doi.org/10.3390/agronomy12010152 - 08 Jan 2022
Cited by 4 | Viewed by 2492
Abstract
The content of chlorophyll, a fundamental component required for photosynthesis in plants, has been widely studied across crop species. In this study, we aimed to evaluate the genetic diversity of 453 peanut accessions. We evaluated the evolutionary relationships using a genome-wide association study [...] Read more.
The content of chlorophyll, a fundamental component required for photosynthesis in plants, has been widely studied across crop species. In this study, we aimed to evaluate the genetic diversity of 453 peanut accessions. We evaluated the evolutionary relationships using a genome-wide association study (GWAS) of leaf color data based on chlorophyll content analysis using the Axiom_Arachis array containing 58K single-nucleotide polymorphisms (SNPs). We identified seven SNPs as being significantly associated with leaf chlorophyll content on the chromosomes Aradu.A02, Aradu.A08, Araip.B02, Araip.B05, Araip.B06, and Araip.B08 in a GAPIT analysis. The SNP AX-176820297 on Araip.B05 was significantly linked with leaf chlorophyll content across the seasons. The Arahy.SDG4EV gene was detected to be in linkage disequilibrium (LD) with the significant SNPs, and its expression was significantly correlated with leaf chlorophyll content. The results of the current study provide useful and fundamental information with which to assess genetic variations in chlorophyll content and can be utilized for further genetic and genomic studies and breeding programs in peanuts. Full article
(This article belongs to the Special Issue Molecular Marker Assisted Crop Breeding)
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17 pages, 2539 KiB  
Article
Genome-Wide Association Study (GWAS) of Mesocotyl Length for Direct Seeding in Rice
by Seong-Gyu Jang, So-Yeon Park, San Mar Lar, Hongjia Zhang, Ah-Rim Lee, Fang-Yuan Cao, Jeonghwan Seo, Tae-Ho Ham, Joohyun Lee and Soon-Wook Kwon
Agronomy 2021, 11(12), 2527; https://doi.org/10.3390/agronomy11122527 - 13 Dec 2021
Cited by 6 | Viewed by 2787
Abstract
Direct seeding is considered an efficient cultivation technology that reduces water use and labor costs. Mesocotyl length is one of the significant traits in cultivation; long mesocotyl is beneficial for the rate and uniformity of seedling emergence. In this study, we used a [...] Read more.
Direct seeding is considered an efficient cultivation technology that reduces water use and labor costs. Mesocotyl length is one of the significant traits in cultivation; long mesocotyl is beneficial for the rate and uniformity of seedling emergence. In this study, we used a core collection of 137 rice accessions to identify quantitative trait loci (QTL) for mesocotyl elongation. A genome-wide association study (GWAS), combined with a principal component analysis (PCA) and a kinship matrix analysis, was conducted for the genotype analysis of 2 million, high-quality single nucleotide polymorphisms (SNPs). Through this GWAS analysis, 11 lead SNPs were confirmed to be associated with mesocotyl length, and a linkage disequilibrium (LD) decay analysis identified the 230 kb exploratory range for the detection of QTLs and candidate genes. Based on the gene expression database and haplotype analysis, five candidate genes (Os01g0269800, Os01g0731100, Os08g0136700, Os08g0137800, and Os08g0137900) were detected to be significantly associated with phenotypic variation. Five candidate gene expressions are reported to be associated with various plant hormone responses. Interestingly, two biotic stress response genes and two copper-containing redox proteins were detected as the candidate genes. The results of this study provide associated SNPs in candidate genes for mesocotyl length and strategies for developing direct seeding in breeding programs. Full article
(This article belongs to the Special Issue Molecular Marker Assisted Crop Breeding)
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13 pages, 1269 KiB  
Article
Identification of Soybean Yield QTL in Irrigated and Rain-Fed Environments
by Geung-Joo Lee, Sungwoo Lee, Tommy E. Carter, Jr., Grover Shannon and H. Roger Boerma
Agronomy 2021, 11(11), 2207; https://doi.org/10.3390/agronomy11112207 - 30 Oct 2021
Cited by 4 | Viewed by 1678
Abstract
Drought is the primary abiotic stress that limits yield of soybean (Glycine max (L.) Merr.). The study aimed to identify yield-related quantitative trait loci (QTLs) in soybeans using a population of 160 F4-derived lines from ‘Hutcheson’ × PI 471938 crosses, [...] Read more.
Drought is the primary abiotic stress that limits yield of soybean (Glycine max (L.) Merr.). The study aimed to identify yield-related quantitative trait loci (QTLs) in soybeans using a population of 160 F4-derived lines from ‘Hutcheson’ × PI 471938 crosses, which were cultivated under rain-fed and irrigated conditions. Seed yield was determined based on a total of nine irrigated and five rain-fed environments over two years. Twenty and twenty-seven SSR markers associated with yield (p ≤ 0.05) were identified in the irrigated and rain-fed environments, respectively. Four markers accounted for 22% of the yield variation in the irrigated environments (IR-YLD) and five markers explained 34% of the yield variation in the rain-fed environments (RF-YLD). Two independent IR-YLD and RF-YLD QTLs on chromosome (Chr) 13 (LG-F) were mapped to the Satt395-Sat_074 interval (4.2 cM) and near Sat_375 (3.0 cM), which explained 8% (LOD = 2.6) and 17% (LOD = 5.5) of the yield variation, respectively. The lines homozygous for the Hutcheson allele at the IR-YLD QTL linked to Sat_074 averaged 100 kg ha−1 higher yield than the lines homozygous for the PI 471938 allele. At two independent RF-YLD QTLs on Chr 13 and Chr 17, the lines homozygous for the PI 471938 alleles were 74 to 101 kg ha−1 higher in yield than the lines homozygous for the Hutcheson alleles. Three of the five significant SSR markers associated with RF-YLD were located in a genomic region known for canopy-wilting QTLs, in which the favorable alleles were inherited from PI 471938. The identification of yield-QTLs under the respective rain-fed and irrigated environments provides knowledge regarding differential responses of yield under different irrigation conditions, which will be helpful in developing high-yielding soybean cultivars. Full article
(This article belongs to the Special Issue Molecular Marker Assisted Crop Breeding)
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16 pages, 2120 KiB  
Article
Comparative Assessment of Effectiveness of Alternative Genotyping Assays for Characterizing Carotenoids Accumulation in Tropical Maize Inbred Lines
by Abdoul-Raouf Sayadi Maazou, Melaku Gedil, Victor O. Adetimirin, Silvestro Meseka, Wende Mengesha, Deborah Babalola, Queen Nkem Offornedo and Abebe Menkir
Agronomy 2021, 11(10), 2022; https://doi.org/10.3390/agronomy11102022 - 09 Oct 2021
Cited by 5 | Viewed by 1629
Abstract
The development of maize varieties with increased concentration of Provitamin A (PVA) is an effective and affordable strategy to combat vitamin A deficiency in developing nations. However, the considerably high cost of carotene analysis poses a major challenge for maize PVA biofortification, prompting [...] Read more.
The development of maize varieties with increased concentration of Provitamin A (PVA) is an effective and affordable strategy to combat vitamin A deficiency in developing nations. However, the considerably high cost of carotene analysis poses a major challenge for maize PVA biofortification, prompting the use of marker-assisted selection. Presently, two types of genotyping with PVA trait-linked functional markers have been developed and extensively used in breeding programs. The two systems are low throughput gel-based genotyping and genotyping with Kompetitive Allele-Specific PCR (KASP) single nucleotide polymorphism (SNPs) markers. Although the KASP SNPs genotyping was developed to replace the gel-based genotyping, studies have not been conducted to compare the effectiveness of the KASP SNPs markers with the gel-based markers. This study was conducted to assess the carotenoid content of 64 tropical PVA biofortified maize inbred lines containing temperate germplasm in their genetic backgrounds and screen them with both gel-based and KASP markers of PSY1, LCYE and crtRB1 genes. Many of the 64 inbred lines had PVA concentrations surpassing the 15 µg/g provitamin A breeding target set by the HarvestPlus Challenge Program. Favorable alleles of crtRB1, crtRB1 and the KASP SNPs markers were detected in 25 inbred lines with high PVA concentrations. Inbred lines with the favorable alleles of LCYE had the highest concentrations of non-PVA carotenoids, whereas those with the favorable alleles of crtRB1 had high levels of PVA carotenoids. Data from the sequenced region of LCYE revealed one SNP in the first intron that clearly differentiated the high and low β-carotene maize inbred lines. The results of our study demonstrate that the automated KASP SNPs markers can replace the gel-based genotyping for screening a large number of early generation maize inbred lines for PVA content. Full article
(This article belongs to the Special Issue Molecular Marker Assisted Crop Breeding)
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