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Agronomy
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Application of Molecular Marker Technology in Crop Breeding
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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: closed (31 March 2023) | Viewed by 21949

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
Special Issues, Collections and Topics in MDPI journals

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

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Related Special Issue

Published Papers (7 papers)

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Research

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15 pages, 3294 KiB  
Article
Genetic Diversity in Oilseed and Vegetable Mustard (Brassica juncea L.) Accessions Revealed by Nuclear and Mitochondrial Molecular Markers
by Dongsuo Zhang, Haibo Yu, Lianliang Gao, Jing Wang, Hui Dong, Yuan Guo and Shengwu Hu
Agronomy 2023, 13(3), 919; https://doi.org/10.3390/agronomy13030919 - 20 Mar 2023
Cited by 3 | Viewed by 2535
Abstract
Genetic diversity analysis is a fundamental work for effective management and utilization of plant germplasm. Brassica juncea is an economically important crop, including both oilseed and vegetable types. In the present study, a total of 99 accessions of Brassicaceae family, including 84 mustard (50 [...] Read more.
Genetic diversity analysis is a fundamental work for effective management and utilization of plant germplasm. Brassica juncea is an economically important crop, including both oilseed and vegetable types. In the present study, a total of 99 accessions of Brassicaceae family, including 84 mustard (50 oilseed and 34 vegetable types) in China and 15 other Brassicaceae accessions were evaluated for their genetic diversity using nuclear and mitochondrial molecular markers. All accessions were evaluated using 18 simple sequence repeats, 20 sequence related amplified polymorphisms, and 7 intron-exon splice junction primers, and in total, 232 polymorphic fragments were obtained. The unweighted pair-group method with arithmetic mean cluster analysis indicated that all accessions could be divided into three major clusters, with cluster I including all 50 oilseed mustard, cluster II including 34 vegetable mustard, and cluster III containing 15 other Brassicaceae accessions. The results of principal component analysis and population structure analysis were in accordance with the cluster result. Molecular variance analysis revealed that the genetic variation was 34.07% among populations and 65.93% within Brassica species, which indicates existence of considerable genetic variation among oilseed and vegetable B. juncea species. Based on an InDel and a SNP locus reported in B. juncea mitochondrial genome, all the 84 B. juncea mitochondrial genomes were divided into three mitotypes (MTs1-3), 22 accessions of MT1, 20 accessions of MT2, and 42 accessions of MT3. In addition, the results of the modified multiplex PCR, Indel and SNP could identify pol-, cam-, nap- (or MT4), Bol-, Bni-, Esa-, and In-cytoplasmic types in 15 other Brassicaceae accessions. Together, oilseed and vegetable B. juncea can be used for broadening the genetic background for each other. Full article
(This article belongs to the Special Issue Application of Molecular Marker Technology in Crop Breeding)
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14 pages, 5817 KiB  
Article
Analysis of Genetic Diversity, Population Structure and Association Mapping for Late Blight Resistance in Potato (Solanum tuberosum L.) Accessions Using SSR Markers
by Vinay Bhardwaj, Ashwani Kumar, Sanjeev Sharma, Baljeet Singh, Poonam, Salej Sood, Bhawna Dipta, Rajender Singh, Sundaresha Siddappa, Ajay Kumar Thakur, Dalamu Dalamu, Ashwani Kumar Sharma, Vinod Kumar, Mehi Lal and Devendra Kumar
Agronomy 2023, 13(2), 294; https://doi.org/10.3390/agronomy13020294 - 18 Jan 2023
Cited by 10 | Viewed by 2596
Abstract
The allelic variations in a diversity panel of 353 potato accessions, including 256 accessions belonging to Solanum tuberosum sub spp. tuberosum, 49 accessions belonging to Solanum tuberosum sub spp. andigena, and 48 Indian potato varieties were analysed using 25 simple sequence [...] Read more.
The allelic variations in a diversity panel of 353 potato accessions, including 256 accessions belonging to Solanum tuberosum sub spp. tuberosum, 49 accessions belonging to Solanum tuberosum sub spp. andigena, and 48 Indian potato varieties were analysed using 25 simple sequence repeat (SSR) markers. The SSR allelic profiles revealed high levels of polymorphism and distinctness among the accessions studied. A total of 343 alleles of 25 SSR markers were observed in the diversity panel of 353 highly diverse tetraploid potato accessions. The number of alleles produced per SSR varied from 8 for the marker STM1053 to 25 for the marker STIKA. The polymorphic information content (PIC) ranged from 0.66 (STG0010) to 0.93 (STM1106) with an average of 0.82. The cluster analysis using the SSR allelic profiles of 353 accessions divided the population into five major groups. The association mapping for late blight resistance identified six markers with the general linear model (GLM), and out of these six markers significance of three markers was reconfirmed with the mixed linear model (MLM). The findings of this study suggest that SSRs are the appropriate markers for evaluating genetic diversity and population structure within different potato germplasm collections. A significant diversity across the tetraploid potato accessions was observed. Moreover, the markers identified in this study could be useful in marker-assisted selection (MAS) breeding in potato for late blight resistance (LBR). Full article
(This article belongs to the Special Issue Application of Molecular Marker Technology in Crop Breeding)
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12 pages, 1422 KiB  
Article
Evaluation of Indian Mustard Genotypes for White Rust Resistance Using BjuWRR1Gene and Their Phenotypic Performance
by Yengkhom Sanatombi Devi, Th. Renuka Devi, Ajay Kumar Thakur, Umakanta Ngangkham, H. Nanita Devi, Pramesh Kh., Bireswar Sinha, Pushparani Senjam, N. Brajendra Singh and Lokesh Kumar Mishra
Agronomy 2022, 12(12), 3122; https://doi.org/10.3390/agronomy12123122 - 8 Dec 2022
Cited by 1 | Viewed by 2928
Abstract
The present investigation was carried out to identify the potential donors of resistant gene(s)/the source of white rust disease in B. juncea using 30 genotypes, including locally adapted accessions and advanced breeding lines. Out of 30 genotypes, ten lines viz. Bio-YSR, CAULC-1, CAULC-2, [...] Read more.
The present investigation was carried out to identify the potential donors of resistant gene(s)/the source of white rust disease in B. juncea using 30 genotypes, including locally adapted accessions and advanced breeding lines. Out of 30 genotypes, ten lines viz. Bio-YSR, CAULC-1, CAULC-2, CAULC-3, CAULC-4, CAURM-2, CAULR-7, CAURM-4, CAURM 4-1, and CAURM 4-2 exhibited a lower PDI value (lesser than mean 10.83) with a superior agronomic performance related with the disease. The evaluation of these ten genotypes for the presence of the BjuWRR1 gene using a gene-based marker depicted the presence of the functional allele of the BjuWRR1 gene in the five genotypes viz., Bio-YSR, CAULC-1, CAULC-3, CAURM 4-1 and CAURM 4-2. When compared with the sequenced amplicon of these genotypes, it is found to be identical with that of an east European Brassica juncea line, Donskaja-IV, the completely resistant genotype against various isolates of Albugo candida. The findings from the present study suggested that besides Bio-YSR, the local lines of Manipur CAULC-1 (Local Yella of Potshangbam) and CAULC-3 (Local Yella of Kakching Lamjao) can be used as the potential white rust resistance sources/donors in disease resistance breeding programmes for the development of elite B. juncea cultivars in the future. In addition to the local lines, two improved advanced lines, viz. CAURM 4-1 and CAURM 4-2, obtained from a hybridization programme, may be further evaluated for releasing resistant varieties against white rust. Full article
(This article belongs to the Special Issue Application of Molecular Marker Technology in Crop Breeding)
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22 pages, 5897 KiB  
Article
Molecular Characterization of Diverse Wheat Genetic Resources for Resistance to Yellow Rust Pathogen (Puccinia striiformis)
by Muhammad Saeed, Muhammad Ibrahim, Waqas Ahmad, Muhammad Tayyab, Safira Attacha, Mudassar Nawaz Khan, Sultan Akbar Jadoon, Syed Jehangir Shah, Shaista Zeb, Liaqat Shah, Fazal Munsif, Ahmad Zubair, Jie Lu, Hongqi Si and Chuanxi Ma
Agronomy 2022, 12(12), 2951; https://doi.org/10.3390/agronomy12122951 - 24 Nov 2022
Cited by 2 | Viewed by 2179
Abstract
Yellow rust (YR) epidemics have affected wheat productivity worldwide. YR resistance (Yr) is eminent in wheat; however, it is continuously invaded by evolving YR pathogen Puccinia striiformis (Pst.). Understanding the Yr genes’ diversity among the available germplasm is paramount to developing [...] Read more.
Yellow rust (YR) epidemics have affected wheat productivity worldwide. YR resistance (Yr) is eminent in wheat; however, it is continuously invaded by evolving YR pathogen Puccinia striiformis (Pst.). Understanding the Yr genes’ diversity among the available germplasm is paramount to developing YR-resistant cultivars. In this study, 14 wheat genotypes were screened for their relative resistance index (RRI) and Yr genes/QTL via linked microsatellite markers. RRI screening categorized the studied genotypes into susceptible (<5; 4.44 ± 0.75), moderate (5–7; 6.11 ± 0.64), and resistant (>7; 8.45 ± 0.25) bulks (p < 0.001). Genetic analysis using 19 polymorphic microsatellite markers revealed 256 alleles, which were divergent among the three resistance bulks. Markers Xbarc7 and Xgwm429 showed the highest allelic diversity in comparison to Xbarc181, Xwmc419, SCAR1400, and Xgwm130. Resistant bulk showed associated alleles at Yr18 gene-linked markers Xgwm295, cssfr6, and csLV34. Other RRI-associated alleles at markers Xbarc7 and Xbarc101 showed weak and moderate linkages, respectively, with the Yr5 gene; whereas, a moderate association was noted for the Yr15 gene-linked marker Xgwm11. Marker Xwe173 linked with the Yr26 gene showed associated alleles among the susceptible bulk. Cross combinations of the parental lines forming recombinant inbred lines (RILs) demonstrated net higher RRI implying favorable allelic recombination. These results support reports and field observations on novel Pst. races that triggered Yr26, Yr5, and Yr15 busts in recent past. This study further implies that pyramiding all stage resistance genes (Yr5, Yr10, Yr15, and Yr26) with adult plant resistance genes (Yr18 and Yr62) should provide sustained YR resistance. The associated alleles at Yr genes-linked markers provide a basis for marker-assisted YR resistance breeding in wheat. Full article
(This article belongs to the Special Issue Application of Molecular Marker Technology in Crop Breeding)
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13 pages, 1305 KiB  
Article
Identification of Low-Light-Resistant Germplasm and Related Loci of Soybean
by Jinfeng Hou, Shuangshuang Wang, Guolei Shan, Lingyun Yuan, Chenggang Wang, Shidong Zhu, Xiaobo Wang and Lijuan Qiu
Agronomy 2022, 12(7), 1483; https://doi.org/10.3390/agronomy12071483 - 21 Jun 2022
Cited by 2 | Viewed by 1882
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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17 pages, 3183 KiB  
Article
Integrating Genome-Wide Association Study with Transcriptomic Analysis to Predict Candidate Genes Controlling Storage Root Flesh Color in Sweet Potato
by Yi Liu, Rui Pan, Wenying Zhang, Jian Lei, Lianjun Wang, Shasha Chai, Xiaojie Jin, Chunhai Jiao and Xinsun Yang
Agronomy 2022, 12(5), 991; https://doi.org/10.3390/agronomy12050991 - 20 Apr 2022
Cited by 3 | Viewed by 2535
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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Review

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23 pages, 2166 KiB  
Review
Transgene-Free Genome Editing for Biotic and Abiotic Stress Resistance in Sugarcane: Prospects and Challenges
by Sakthivel Surya Krishna, S R Harish Chandar, Maruthachalam Ravi, Ramanathan Valarmathi, Kasirajan Lakshmi, Perumal Thirugnanasambandam Prathima, Ramaswamy Manimekalai, Rasappa Viswanathan, Govindkurup Hemaprabha and Chinnaswamy Appunu
Agronomy 2023, 13(4), 1000; https://doi.org/10.3390/agronomy13041000 - 29 Mar 2023
Cited by 10 | Viewed by 5492
Abstract
Sugarcane (Saccharum spp.) is one of the most valuable food and industrial crops. Its production is constrained due to major biotic (fungi, bacteria, viruses and insect pests) and abiotic (drought, salt, cold/heat, water logging and heavy metals) stresses. The ever-increasing demand for [...] Read more.
Sugarcane (Saccharum spp.) is one of the most valuable food and industrial crops. Its production is constrained due to major biotic (fungi, bacteria, viruses and insect pests) and abiotic (drought, salt, cold/heat, water logging and heavy metals) stresses. The ever-increasing demand for sugar and biofuel and the rise of new pest and disease variants call for the use of innovative technologies to speed up the sugarcane genetic improvement process. Developing new cultivars through conventional breeding techniques requires much time and resources. The advent of CRISPR/Cas genome editing technology enables the creation of new cultivars with improved resistance/tolerance to various biotic and abiotic stresses. The presence of genome editing cassette inside the genome of genome-edited plants hinders commercial exploitation due to regulatory issues. However, this limitation can be overcome by using transgene-free genome editing techniques. Transgene-free genome editing approaches, such as delivery of the RNPs through biolistics or protoplast fusion, virus-induced genome editing (VIGE), transient expression of CRISPR/Cas reagents through Agrobacterium-mediated transformation and other approaches, are discussed. A well-established PCR-based assay and advanced screening systems such as visual marker system and Transgene killer CRISPR system (TKC) rapidly identify transgene-free genome edits. These advancements in CRISPR/Cas technology speed up the creation of genome-edited climate-smart cultivars that combat various biotic and abiotic stresses and produce good yields under ever-changing conditions. Full article
(This article belongs to the Special Issue Application of Molecular Marker Technology in Crop Breeding)
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