Molecular Markers and Marker-Assisted Selection in Crop Plants

Kamaluddin, .; Khan, M. A.; Kiran, Usha; Ali, Athar; Abdin, Malik Zainul; Zargar, M. Y.; Ahmad, Shahid; Sofi, Parvaze A.; Gulzar, Shazia

doi:10.1007/978-981-10-2961-5_12

Cited by 8 publications

(5 citation statements)

References 174 publications

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“…SSR markers located at a specific position of wheat chromosome could be regarded as tags for the presence of chromosomes (arms) ( Röder et al, 1998 ). EST-STS markers were designed from coding DNA and were generally highly conserved, so they could be used for comparative genomic studies between distant species ( Kamaluddin et al, 2017 ). In this study, we found that SSRs on 3D chromosomes amplified D genome-specific bands in wheat parent 7182, but not in lines DH109 and DM131.…”

Section: Discussionmentioning

confidence: 99%

“…Molecular marker-assisted selection has three main categories comprising markers based on molecular hybridization, e.g., restriction fragment length polymorphism and variable number of tandem repeat; markers based on PCR technology, e.g., random amplified polymorphism DNA and SSR; and markers based on high-throughput DNA sequence, e.g., SNP arrays and specific-locus amplified fragment sequencing (SLAF-seq) ( He et al, 2003 ; Varshney et al, 2005 ; Kamaluddin et al, 2017 ). Among them, SNP arrays are likely to be the most important tool in gene mapping and study the relationship of species ( Zhou et al, 2018 ; Zhao et al, 2019 ).…”

Section: Discussionmentioning

confidence: 99%

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Molecular Cytogenetic and Agronomic Characterization of the Similarities and Differences Between Wheat–Leymus mollis Trin. and Wheat–Psathyrostachys huashanica Keng 3Ns (3D) Substitution Lines

Cheng

et al. 2021

Front. Plant Sci.

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Psathyrostachys huashanica Keng (2n = 2x = 14, NsNs) and Leymus mollis Trin. (2n = 4x = 28, NsNsXmXm) are valuable resources for wheat breeding improvement as they share the Ns genome, which contains diverse resistance genes. To explore the behaviors and traits of Ns chromosomes from the two species in wheat background, a series of wheat–P. huashanica and wheat–L. mollis substitution lines were developed. In the present study, line DH109 (F7 progeny of wheat–P. huashanica heptaploid line H8911 × durum wheat Trs-372) and line DM131 (F8 progeny of wheat–L. mollis octoploid line M842 × durum wheat Trs-372) were selected. Cytological observation combined with genomic in situ hybridization experiments showed that DH109 and DM131 each had 20 pairs of wheat chromosomes plus a pair of alien chromosomes (Ns chromosome), and the pair of alien chromosomes showed stable inheritance. Multiple molecular markers and wheat 55K SNP array demonstrated that a pair of wheat 3D chromosome in DH109 and in DM131 was substituted by a pair of P. huashanica 3Ns chromosome and a pair of L. mollis 3Ns chromosome, respectively. Fluorescence in situ hybridization (FISH) analysis confirmed that wheat 3D chromosomes were absent from DH109 and DM131, and chromosomal FISH karyotypes of wheat 3D, P. huashanica 3Ns, and L. mollis 3Ns were different. Moreover, the two lines had many differences in agronomic traits. Comparing with their wheat parents, DH109 expressed superior resistance to powdery mildew and fusarium head blight, whereas DM131 had powdery mildew resistance, longer spike, and more tiller number. Therefore, Ns genome from P. huashanica and L. mollis might have some different effects. The two novel wheat–alien substitution lines provide new ideas and resources for disease resistance and high-yield breeding on further utilization of 3Ns chromosomes of P. huashanica or L. mollis.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Molecular Cytogenetic and Agronomic Characterization of the Similarities and Differences Between Wheat–Leymus mollis Trin. and Wheat–Psathyrostachys huashanica Keng 3Ns (3D) Substitution Lines

Cheng

et al. 2021

Front. Plant Sci.

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“…Molecular markers have allowed the detailed study of germplasm collections, revealing the history of crop domestication, discovering novel genetic diversity [ 42 ], and improving the efficiency of conventional plant breeding schemes through marker-assisted and genomic selection [ 43 – 45 ]. Markers such as COSIIs, IRGs, and SSRs have been used for genetic diversity studies in Colombian cape gooseberry populations, due to their highly polymorphic nature [ 22 , 46 ].…”

Section: Discussionmentioning

confidence: 99%

Optimization of the genotyping‐by‐sequencing SNP calling for diversity analysis in cape gooseberry (Physalis peruviana L.) and related taxa

et al. 2020

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A robust Genotyping-By-Sequencing (GBS) pipeline platform was examined to provide accurate discovery of Single Nucleotide Polymorphisms (SNPs) in a cape gooseberry (Physalis peruviana L.) and related taxa germplasm collection. A total of 176 accessions representing, wild, weedy, and commercial cultivars as well as related taxa from the Colombian germplasm bank and other world repositories were screened using GBS. The pipeline parameters mnLCov of 0.5 and a mnScov of 0.7, tomato and potato genomes, and cape gooseberry transcriptome for read alignments, were selected to better assess diversity and population structure in cape gooseberry and related taxa. A total of 7,425 SNPs, derived from P. peruviana common tags (unique 64 bp sequences shared between selected species), were used. Within P. peruviana, five subpopulations with a high genetic diversity and allele fixation (H E : 0.35 to 0.36 and F IS :-0.11 to-0.01, respectively) were detected. Conversely, low genetic differentiation (F ST : 0.01 to 0.05) was also observed, indicating a high gene flow among subpopulations. These results contribute to the establishment of adequate conservation and breeding strategies for Cape gooseberry and closely related Physalis species.

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“…Conversely, molecular characterization is unaffected by environmental factors and provides useful and accurate complementary genetic information [ 19 ]. There has been extensive application of molecular markers, including mapping of quantitative trait loci (QTL), gene cloning, studying of marker–trait associations, genetic diversity, population structure, and marker-assisted selection (MAS) for genetic and breeding research [ 20 , 21 ]. MAS relies on molecular markers to select superior phenotypic traits based on genotypes, and for its effectiveness, the significance of identifying linked markers and their corresponding genetic regions has been highlighted [ 22 ].…”

Section: Introductionmentioning

confidence: 99%

Association Mapping for Evaluation of Population Structure, Genetic Diversity, and Physiochemical Traits in Drought-Stressed Maize Germplasm Using SSR Markers

Ilyas,

Park,

Jang

et al. 2023

Plants

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Globally, maize is one of the most consumed crops along with rice and wheat. However, maize is sensitive to different abiotic stress factors, such as drought, which have a significant impact on its production. The aims of this study were to investigate (1) genetic variation among 41 maize-inbred lines and the relationships among them and (2) significant marker–trait associations (SMTAs) between 7 selected physiochemical traits and 200 simple sequence repeat (SSR) markers to examine the genetics of these traits. A total of 1023 alleles were identified among the 41 maize-inbred lines using the 200 SSR loci, with a mean of 5.1 alleles per locus. The average major allele frequency, gene diversity, and polymorphism information content were 0.498, 0.627, and 0.579, respectively. The population structure analysis based on the 200 SSR loci divided the maize germplasm into two primary groups with an admixed group. Moreover, this study identified, respectively, 85 SMTAs and 31 SMTAs using a general linear model (Q GLM) and a mixed linear model (Q + K MLM) with statistically significant (p < 0.05 and <0.01) associations with the seven physiochemical traits (caffeic acid content, chlorogenic acid content, gallic acid content, ferulic acid content, 2,2-diphenyl-1-picrylhydrazyl free radical scavenging activity, leaf relative moisture content, total phenolic content). These SSR markers were highly correlated with one or more of the seven physiochemical traits. This study provides insights into the genetics of the 41 maize-inbred lines and their seven physiochemical traits and will be of assistance to breeders in the marker-assisted selection of maize for breeding programs.

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Molecular Markers and Marker-Assisted Selection in Crop Plants

Cited by 8 publications

References 174 publications

Molecular Cytogenetic and Agronomic Characterization of the Similarities and Differences Between Wheat–Leymus mollis Trin. and Wheat–Psathyrostachys huashanica Keng 3Ns (3D) Substitution Lines

Molecular Cytogenetic and Agronomic Characterization of the Similarities and Differences Between Wheat–Leymus mollis Trin. and Wheat–Psathyrostachys huashanica Keng 3Ns (3D) Substitution Lines

Optimization of the genotyping‐by‐sequencing SNP calling for diversity analysis in cape gooseberry (Physalis peruviana L.) and related taxa

Association Mapping for Evaluation of Population Structure, Genetic Diversity, and Physiochemical Traits in Drought-Stressed Maize Germplasm Using SSR Markers

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