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Agronomy
Special Issues
Marker Assisted Selection and Molecular Breeding in Major Crops
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Marker Assisted Selection and Molecular Breeding in Major Crops

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

Deadline for manuscript submissions: closed (15 September 2024) | Viewed by 5134

Special Issue Editor

Dr. Shikai Hu

E-Mail Website
Guest Editor
China National Rice Improvement Centre, China National Rice Research Institute, Hangzhou 310006, China
Interests: rice genetic improvement; rice grain quality traits; rice molecular design breeding

Special Issue Information

Dear Colleagues,

With the rapid increase in the population and the deterioration of the environment, we are faced with an increasingly serious food crisis. An effective way to alleviate the food crisis is to cultivate high-yield, high-quality. and wide-adaptability crop varieties faster. In recent years, with the development of molecular biology technology, molecular markers have undergone many updates. The application of molecular markers has greatly improved the breeding selection efficiency, shortened the breeding cycle, and made the breeding leap from the experience breeding to molecular breeding eras.

In this Special Issue, we will focus on advances in the molecular breeding of major crops, such as food, oil, and economic crops. All the original research, opinions, methodological papers, and reviews on Marker-assisted Selection and Molecular Breeding are welcome.

Dr. Shikai Hu
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 quality improvement
  • crop stress tolerance improvement
  • crop multi-trait synergistic improvement
  • efficient molecular breeding techniques and methods

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Published Papers (5 papers)

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Research

13 pages, 2898 KiB  
Article
Development and Trait-Based Molecular Characterization of Thermosensitive Genic Male-Sterile Rice (Oryza sativa L.) Lines at Texas A&M AgriLife Research
by Darlene L. Sanchez, Stanley Omar PB. Samonte, Kimberly S. Ponce, Zongbu Yan and Lloyd T. Wilson
Agronomy 2024, 14(12), 2773; https://doi.org/10.3390/agronomy14122773 - 22 Nov 2024
Viewed by 1
Abstract
This study aimed to develop and genetically characterize thermosensitive genic male-sterility (TGMS) lines for use in hybrid rice (Oryza sativa L.) breeding. Male-sterile F2 to F4 generation lines were screened during the high-temperature summer season, and ratoon crops of selected [...] Read more.
This study aimed to develop and genetically characterize thermosensitive genic male-sterility (TGMS) lines for use in hybrid rice (Oryza sativa L.) breeding. Male-sterile F2 to F4 generation lines were screened during the high-temperature summer season, and ratoon crops of selected male-sterile rows were harvested for pure seed. Sixty-six F5 TGMS lines were genotyped using DNA markers controlling 16 traits from the LSU80 QA/QC Rice PlexSeq SNP Panel. Ten TGMS lines with desirable traits that included semidwarf, glabrous, non-aromatic, long-grain, narrow brown leaf spot resistance, and blast resistance genes were selected for further genotypic characterization using markers for low chalkiness (chalk5), wide compatibility (S5-n), cold tolerance (qSCT-11 and qCST-12), and anaerobic germination (AG1 and AG2). TGMS lines TIL21051S and TIL21052S possess favorable alleles for each of the genes evaluated in this study and are desirable parents for two-line hybrid breeding in the southeast United States. TIL21044S, TIL21095S, TIL21060S, and TIL21066S each contain three blast resistance genes and have potential as parental lines. TIL21014S-2, TIL21015S, and TIL21016S-1 include the fgr allele for aroma and can also be used as parental lines for aromatic two-line hybrids. Full article
(This article belongs to the Special Issue Marker Assisted Selection and Molecular Breeding in Major Crops)
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23 pages, 3149 KiB  
Article
Genetic Evaluation of Kazakhstani Potato Germplasm for Pathogen and Pest Resistance Using DNA Markers
by Kamila Adilbayeva, Ruslan Moisseyev, Mariya Kolchenko, Roza Kenzhebekova, Vadim Khassanov, Bibigul Beisembina, Moldir Azhimakhan, Zhursinkul Tokbergenova, Dinara Sharipova, Valeriy Krasavin, Alexandr Pozharskiy and Dilyara Gritsenko
Agronomy 2024, 14(9), 1923; https://doi.org/10.3390/agronomy14091923 - 27 Aug 2024
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Abstract
Potato is one of the most consumed crops worldwide. One strategy aimed at pathogen and pest management is the cultivation of resistant varieties. In this study, 352 genotypes from the Kazakhstan potato germplasm collection were screened for the presence of loci for resistance [...] Read more.
Potato is one of the most consumed crops worldwide. One strategy aimed at pathogen and pest management is the cultivation of resistant varieties. In this study, 352 genotypes from the Kazakhstan potato germplasm collection were screened for the presence of loci for resistance to the most harmful pathogens and pests using 30 DNA markers. ‘Rucheek’ and ‘Spiridon’, among the top global varieties, and ‘Janaisan’ and ‘Fedor’, among the top local varieties, were identified as bearing the most resistance loci in the collection, with at least 14 markers each. The specimens carrying the genes Ryadg (ADG1, ADG2), Nb (SPUD237), Ns (SC811, CP16), Rpi-phu1 (GP94), and GroV1 (X02), which demonstrate confirmed resistance to PVY, PVA, PVX, PVS, Phytophthora infestans, and Globodera rostochiensis, were most frequently found in the collection. Loci for resistance to Synchytrium endobioticum and Globodera pallida were less introgressed into the Kazakhstani cultivars and were almost absent in the germplasm collection. The less abundant loci found in the current potato collection were Ryadg (RysC3), Gro1-4 (Gro1-4), and Rladg (RGASC850). Screening of the potato collection showed that the markers SPUD237, CP60, 45/X1, and CT214 generated additional polymorphic amplicons, while markers Nl25, C237, GP179, and GP122718 were less applicable in robust large-scale screening. The results from this study may greatly contribute to marker-assisted selection and gene pyramiding strategies aimed at developing new potato varieties with multiple resistance to biotic stress Full article
(This article belongs to the Special Issue Marker Assisted Selection and Molecular Breeding in Major Crops)
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19 pages, 3223 KiB  
Article
Genome-Wide Association Study of Yield-Related Traits in a Nested Association Mapping Population Grown in Kazakhstan
by Akerke Amalova, Simon Griffiths, Saule Abugalieva and Yerlan Turuspekov
Agronomy 2024, 14(8), 1848; https://doi.org/10.3390/agronomy14081848 - 21 Aug 2024
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Abstract
This study evaluated 290 recombinant inbred lines (RILs) from the Nested Association Mapping (NAM) population in the UK, consisting of 24 hybrid families. All genotypes were grown in Southeastern Kazakhstan (Kazakh Research Institute of Agriculture and Plant Growing, Almaty region, 2021–2022) and Northern [...] Read more.
This study evaluated 290 recombinant inbred lines (RILs) from the Nested Association Mapping (NAM) population in the UK, consisting of 24 hybrid families. All genotypes were grown in Southeastern Kazakhstan (Kazakh Research Institute of Agriculture and Plant Growing, Almaty region, 2021–2022) and Northern Kazakhstan (Alexandr Barayev Scientific-Production Center for Grain Farming, Akmola region, 2020). The studied traits included six yield-related characteristics: spike length (SL, cm), number of productive spikes per plant (NPS, pcs), number of kernels per spike (NKS, pcs), weight of kernels per spike (WKS, g), thousand kernel weight (TKW, g), and yield per square meter (YM2, g/m2). The significant phenotypic variability among genotypes was observed, which was suitable for the genome-wide association study of yield-related traits. Pearson’s index showed positive correlations among most yield-related traits, although a negative correlation was found between NKS and TKW in southeastern regions, and no correlation was recorded for northern regions. Top-performing RILs, surpassing local checks, were identified for NKS, TKW, and YM2, suggesting their potential for breeding programs. The application of GWAS allowed the identification of 72 quantitative trait loci (QTLs), including 36 QTLs in the southeastern region, 16 QTLs in the northern region, and 19 in both locations. Eleven QTLs matched those reported in previous QTL mapping studies and GWAS for studied traits. The results can be used for further studies related to the adaptation and productivity of wheat in breeding projects for higher grain productivity. Full article
(This article belongs to the Special Issue Marker Assisted Selection and Molecular Breeding in Major Crops)
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12 pages, 1447 KiB  
Article
Genetic Diversity, Linkage Disequilibrium, and Population Structure in a Common Bean Reference Collection
by Daniel Ambachew, Jorge Mario Londoño, Nohra Rodriguez Castillo, Asrat Asfaw and Matthew Wohlgemuth Blair
Agronomy 2024, 14(5), 985; https://doi.org/10.3390/agronomy14050985 - 8 May 2024
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Abstract
An in-depth understanding of the extent and pattern of genetic diversity and population structure in crop populations is of paramount importance for any crop improvement program to efficiently promote the translation of genetic diversity into genetic gain. A reference collection of 150 common [...] Read more.
An in-depth understanding of the extent and pattern of genetic diversity and population structure in crop populations is of paramount importance for any crop improvement program to efficiently promote the translation of genetic diversity into genetic gain. A reference collection of 150 common bean genotypes selected from the International Center for Tropical Agriculture’s global core collection was evaluated using single-nucleotide polymorphism (SNP) markers to quantify the amount of genetic diversity, linkage disequilibrium, and population structure. The cultivars and landraces of the collection were diverse and originated from 14 countries, and wild accessions were used as controls for each gene pool. The collection was genotyped using an SNP array, generating a total of 5398 locus calls distributed across the entire bean genome. The SNP data quality was checked, and two datasets were generated. The first dataset (Dataset_1) comprised a set of 5108 SNPs and 150 genotypes after filtering for 10% missing alleles and an MAF < 0.05. The second dataset (Dataset_2) comprised a set of 2300 SNPs that remained after removing any null-allele SNPs and LD pruning for a criterion of r2 < 0.2. Dataset_1 was used for a principal coordinate analysis (PCoA), phylogenetic relationship determination, an analysis of molecular variance (AMOVA), and a discriminant analysis of principal components. Dataset_2 was used for a population structure analysis using STRUCTURE software and is proposed for a genome-wide association study (GWAS). The population structure analysis split the reference collection into two subpopulations according to an Andean or Mesoamerican gene pool. The Mesoamerican populations displayed higher genetic differentiation and tended to split into more groups that were somewhat aligned with common bean races. Andean beans were characterized by a larger average LD but lower LD percentage, a small average genetic distance between members of the population, and a higher major allele frequency, which suggested narrower genetic diversity compared to the Mesoamerican gene pool. In conclusion, the results indicated the presence of high genetic diversity, which is useful for a GWAS. However, the presence of significant linkage disequilibrium requires that genetic distance be considered as a co-factor for any further genetic studies. Overall, the molecular variation observed in the genotypes shows that this reference collection is valuable as a genebank-derived diversity panel which is useful for marker trait association studies. Full article
(This article belongs to the Special Issue Marker Assisted Selection and Molecular Breeding in Major Crops)
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20 pages, 2552 KiB  
Article
Incorporation of Photoperiod Insensitivity and High-Yield Genes into an Indigenous Rice Variety from Myanmar, Paw San Hmwe
by Khin Thanda Win, Moe Moe Hlaing, Aye Lae Lae Hlaing, Zin Thu Zar Maung, Khaing Nwe Oo, Thinzar Nwe, Sandar Moe, Thein Lin, Ohm Mar Saw, Thado Aung, Mai Swe Swe, San Mar Lar, Ei Shwe Sin, Yoshiyuki Yamagata, Enrique R. Angeles, Yuji Matsue, Hideshi Yasui, Min San Thein, Naing Kyi Win, Motoyuki Ashikari and Atsushi Yoshimuraadd Show full author list remove Hide full author list
Agronomy 2024, 14(3), 632; https://doi.org/10.3390/agronomy14030632 - 20 Mar 2024
Viewed by 1509
Abstract
Paw San Hmwe (PSH) is an indigenous rice variety from Myanmar with a good taste, a pleasant fragrance, and excellent elongation ability during cooking. However, its low yield potential and strong photoperiod sensitivity reduce its productivity, and it is vulnerable to climate changes [...] Read more.
Paw San Hmwe (PSH) is an indigenous rice variety from Myanmar with a good taste, a pleasant fragrance, and excellent elongation ability during cooking. However, its low yield potential and strong photoperiod sensitivity reduce its productivity, and it is vulnerable to climate changes during growth. To improve the photoperiod insensitivity, yield, and plant stature of PSH, the high-yield genes Grain number 1a (Gn1a) and Wealthy Farmer’s Panicle (WFP), together with the photoperiod insensitivity trait, were introgressed into PSH via marker-assisted backcross breeding and phenotype selection. For the photoperiod insensitivity trait, phenotypic selection was performed under long-day conditions during the dry season. After foreground selection of Gn1a and WFP via simple sequence repeat genotyping, genotyping-by-sequencing was conducted to validate the introgression of target genes and determine the recurrent parent genome recovery of the selected lines. The improved lines were insensitive to photoperiod, and the Gn1a and WFP introgression lines showed significantly higher numbers of primary panicle branches and spikelets per panicle than the recurrent parent, with comparative similarity in cooking and eating qualities. This study successfully improved PSH by decreasing its photoperiod sensitivity and introducing high-yield genes via marker-assisted selection. The developed lines can be used for crop rotation and double-season cropping of better-quality rice. Full article
(This article belongs to the Special Issue Marker Assisted Selection and Molecular Breeding in Major Crops)
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