Molecular Marker-Assisted Technologies for Crop Breeding

A special issue of Plants (ISSN 2223-7747). This special issue belongs to the section "Plant Molecular Biology".

Deadline for manuscript submissions: 31 August 2024 | Viewed by 5824

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Guest Editor
Department of Applied Plant Sciences, College of Agriculture and Life Sciences, Kangwon National University, Chuncheon 24341, Republic of Korea
Interests: genetics; molecular breeding science

Special Issue Information

Dear Colleagues,

Maize is among leading global cereals, encompassing all agroecological zones of South Sudan; however, farmers’ fields yield very low amounts, which can only be accredited to their dependency on undeveloped varieties. When it comes to maize, small-scale farmers in South Sudan practice subsistence agriculture. In the current study, the genetic diversity and population structure were investigated among 37 South Sudan landrace maize accessions collected from farmers’ fields using 27 SSR markers. A total of (200) alleles was revealed with an average of (3.0) alleles per locus, ranging from 7.4 to 13.0 alleles per locus. The observed heterozygosity values ranged from 0.06 to 0.91, with an average of (0.35). High PIC values were identified with a mean of 0.69, which showed the informativeness of the chosen SSR loci. A genetic structure analysis revealed a moderate genetic differentiation of 0.16 within maize populations with a fixation index (Fst), while a very high genetic differentiation of 0.37 mean Fst was recorded among a group of populations in three regions. The analysis of the unweighted pair group method with an arithmetic mean (UPGMA) dendrogram clustered the 37 maize accessions into three groups with a 43% genetic similarity. The clustering pattern of maize accessions was comparatively consistent with their collection areas. The findings of this study can provide maize breeders with a superior understanding of maize diversification, as well as the reservation of genetic resources to be used in the selection of advantageous and useful resources for the development of maize varieties in South Sudan.

Dr. Ju Kyong Lee
Guest Editor

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Keywords

  • maize
  • landrace accession
  • agroecological zone
  • SSR marker
  • genetic diversity
  • population structure
  • UPGMA dendrogram

Published Papers (3 papers)

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Research

16 pages, 1628 KiB  
Article
Association Mapping of Amylose Content in Maize RIL Population Using SSR and SNP Markers
by Kyu Jin Sa, Hyeon Park, So Jung Jang and Ju Kyong Lee
Plants 2023, 12(2), 239; https://doi.org/10.3390/plants12020239 - 4 Jan 2023
Cited by 3 | Viewed by 1989
Abstract
The ratio of amylose to amylopectin in maize kernel starch is important for the appearance, structure, and quality of food products and processing. This study aimed to identify quantitative trait loci (QTLs) controlling amylose content in maize through association mapping with simple sequence [...] Read more.
The ratio of amylose to amylopectin in maize kernel starch is important for the appearance, structure, and quality of food products and processing. This study aimed to identify quantitative trait loci (QTLs) controlling amylose content in maize through association mapping with simple sequence repeat (SSR) and single-nucleotide polymorphism (SNP) markers. The average value of amylose content for an 80-recombinant-inbred-line (RIL) population was 8.8 ± 0.7%, ranging from 2.1 to 15.9%. We used two different analyses—Q + K and PCA + K mixed linear models (MLMs)—and found 38 (35 SNP and 3 SSR) and 32 (29 SNP and 3 SSR) marker–trait associations (MTAs) associated with amylose content. A total of 34 (31 SNP and 3 SSR) and 28 (25 SNP and 3 SSR) MTAs were confirmed in the Q + K and PCA + K MLMs, respectively. This study detected some candidate genes for amylose content, such as GRMZM2G118690-encoding BBR/BPC transcription factor, which is used for the control of seed development and is associated with the amylose content of rice. GRMZM5G830776-encoding SNARE-interacting protein (KEULE) and the uncharacterized marker PUT-163a-18172151-1376 were significant with higher R2 value in two difference methods. GRMZM2G092296 were also significantly associated with amylose content in this study. This study focused on amylose content using a RIL population derived from dent and waxy inbred lines using molecular markers. Future studies would be of benefit for investigating the physical linkage between starch synthesis genes using SNP and SSR markers, which would help to build a more detailed genetic map and provide new insights into gene regulation of agriculturally important traits. Full article
(This article belongs to the Special Issue Molecular Marker-Assisted Technologies for Crop Breeding)
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15 pages, 1114 KiB  
Article
Utilization of Novel Perilla SSR Markers to Assess the Genetic Diversity of Native Perilla Germplasm Accessions Collected from South Korea
by Zhen Yu Fu, Kyu Jin Sa, Hyeon Park, So Jung Jang, Yeon Joon Kim and Ju Kyong Lee
Plants 2022, 11(21), 2974; https://doi.org/10.3390/plants11212974 - 3 Nov 2022
Cited by 5 | Viewed by 1357
Abstract
The Perilla crop is highly regarded in South Korea, both as a health food and traditional food. However, there is still a lack of Perilla SSR primer sets (PSPSs) for studying genetic variation among accessions of cultivated and weedy types of Perilla crop [...] Read more.
The Perilla crop is highly regarded in South Korea, both as a health food and traditional food. However, there is still a lack of Perilla SSR primer sets (PSPSs) for studying genetic variation among accessions of cultivated and weedy types of Perilla crop (CWTPC) from South Korea. In this study, 30 PSPSs were newly developed based on transcriptome contigs in P. frutescens, and 17 of these PSPSs were used to study the genetic diversity, phylogenetic relationships and structure population among 90 accessions of the CWTPC collected from South Korea. A total of 100 alleles were detected from selected 17 PSPSs, with an average of 5.9 alleles per locus. The gene diversity (GD) ranged from 0.164 to 0.831, with an average of 0.549. The average GD values from the cultivated var. frutescens, weedy var. frutescens, and weedy var. crispa, were 0.331, 0.588, and 0.389 respectively. In addition, most variance shown by Perilla SSR markers was within a population (73%). An analysis of the population structure and phylogenetic relationships showed that the genetic relationship among accessions of the weedy var. frutescens and weedy var. crispa is closer than that for the accessions of the cultivated var. frutescens. Based on association analysis between 17 PSPSs and three seed traits in 90 Perilla accessions, we detected 11 PSPSs that together were associated with the seed size and seed hardness traits. Therefore, the newly developed PSPSs will be useful for analyzing genetic variation among accessions of the CWTPC, association mapping, and selection of important morphological traits in Perilla crop breeding programs. Full article
(This article belongs to the Special Issue Molecular Marker-Assisted Technologies for Crop Breeding)
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13 pages, 1946 KiB  
Article
Genetic Diversity and Population Structure of Normal Maize Germplasm Collected in South Sudan Revealed by SSR Markers
by Emmanuel Andrea Mathiang, Kyu Jin Sa, Hyeon Park, Yeon Joon Kim and Ju Kyong Lee
Plants 2022, 11(20), 2787; https://doi.org/10.3390/plants11202787 - 20 Oct 2022
Cited by 9 | Viewed by 1727
Abstract
Maize is one of the leading global cereals, and in South Sudan maize cultivation occurs in nearly all of the country’s agro-ecological zones. Despite its widespread cultivation, farmers in South Sudan depend on undeveloped varieties, which results in very low yields in the [...] Read more.
Maize is one of the leading global cereals, and in South Sudan maize cultivation occurs in nearly all of the country’s agro-ecological zones. Despite its widespread cultivation, farmers in South Sudan depend on undeveloped varieties, which results in very low yields in the field. In the current study, 27 simple sequence repeat (SSR) markers were used to investigate genetic diversity and population structures among 37 landrace maize accessions collected from farmers’ fields in South Sudan. In total, 200 alleles were revealed with an average of 7.4 alleles per locus and a range from 3.0 to 13.0 alleles per locus. The observed heterozygosity values ranged from 0.06 to 0.91 with an average of 0.35. High polymorphic information content (PIC) values were identified with a mean of 0.69, which indicates the informativeness of the chosen SSR loci. Genetic structure analysis revealed a moderate genetic differentiation among the maize populations with a fixation index of 0.16, while there was very high genetic differentiation within the groups of populations of three regions with a mean fixation index (F) of 0.37. An unweighted pair group method with an arithmetic mean (UPGMA) dendrogram clustered the 37 maize accessions into three groups with 43% genetic similarity. The clustering pattern of the maize accessions was moderately consistent with their collection area. The findings of this study will provide maize breeders with a better understanding of maize diversification as well as a reserve of genetic resources for use in the selection of advantageous and useful resources for the development of maize varieties in South Sudan. Full article
(This article belongs to the Special Issue Molecular Marker-Assisted Technologies for Crop Breeding)
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