Development of SLAF-Sequence and Multiplex SNaPshot Panels for Population Genetic Diversity Analysis and Construction of DNA Fingerprints for Sugarcane

Zhang, Hui; Lin, Pingping; Liu, Yanming; Huang, Chaohua; Huang, Guoqiang; Jiang, Hongtao; Xu, Ling; Deng, Zuhu; Zhao, Xuhong

doi:10.3390/genes13081477

Cited by 11 publications

(6 citation statements)

References 61 publications

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“…The phenotype is an important manifestation of genetic variation and can directly indicate functional gene diversity [ 22 , 26 ]. In sugarcane, many molecular markers based on genetic diversity have been implemented, such as SSRs [ 27 ], RAPDs [ 28 ], and SNPs [ 29 ], and facilitate the determination of the genetic variability degree occurring among conventional progenitor species, commercial cultivars, and exotic germplasm [ 30 , 31 ]. However, no effective linkage relationship has been established between agronomic traits and molecular markers of sugarcane due to the complexity of the sugarcane genome and the laborious phenotypic measurements at the population level [ 5 , 16 , 31 , 32 ].…”

Section: Discussionmentioning

confidence: 99%

Evaluation of a Sugarcane (Saccharum spp.) Hybrid F1 Population Phenotypic Diversity and Construction of a Rapid Sucrose Yield Estimation Model for Breeding

Kong

et al. 2023

Plants

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Sugarcane is the major sugar-producing crop worldwide, and hybrid F1 populations are the primary populations used in breeding. Challenged by the sugarcane genome’s complexity and the sucrose yield’s quantitative nature, phenotypic selection is still the most commonly used approach for high-sucrose yield sugarcane breeding. In this study, a hybrid F1 population containing 135 hybrids was constructed and evaluated for 11 traits (sucrose yield (SY) and its related traits) in a randomized complete-block design during two consecutive growing seasons. The results revealed that all the traits exhibited distinct variation, with the coefficient of variation (CV) ranging from 0.09 to 0.35, the Shannon-Wiener diversity index (H′) ranging between 2.64 and 2.98, and the broad-sense heritability ranging from 0.75 to 0.84. Correlation analysis revealed complex correlations between the traits, with 30 trait pairs being significantly correlated. Eight traits, including stalk number (SN), stalk diameter (SD), internode length (IL), stalk height (SH), stalk weight (SW), Brix (B), sucrose content (SC), and yield (Y), were significantly positively correlated with sucrose yield (SY). Cluster analysis based on the 11 traits divided the 135 F1 hybrids into three groups, with 55 hybrids in Group I, 69 hybrids in Group II, and 11 hybrids in Group III. The principal component analysis indicated that the values of the first four major components’ vectors were greater than 1 and the cumulative contribution rate reached 80.93%. Based on the main component values of all samples, 24 F1 genotypes had greater values than the high-yielding parent ‘ROC22’ and were selected for the next breeding stage. A rapid sucrose yield estimation equation was established using four easily measured sucrose yield-related traits through multivariable linear stepwise regression. The model was subsequently confirmed using 26 sugarcane cultivars and 24 F1 hybrids. This study concludes that the sugarcane F1 population holds great genetic diversity in sucrose yield-related traits. The sucrose yield estimation model, ySY=2.01xSN+8.32xSD+0.79xB+3.44xSH−47.64, can aid to breed sugarcane varieties with high sucrose yield.

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Section: Discussionmentioning

confidence: 99%

Evaluation of a Sugarcane (Saccharum spp.) Hybrid F1 Population Phenotypic Diversity and Construction of a Rapid Sucrose Yield Estimation Model for Breeding

Kong

et al. 2023

Plants

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“…The principles of the selective digestion plan are as follows: (1) The proportion of digestion SLAF tags located in repeat sequences should be as low as possible; (2) the SLAF tags were evenly distributed on the genome as far as possible; (3) the consistency of the fragment length should be maintained with the specific test system; and (4) the number of enzyme‐cut SLAF tags obtained met the expected number of tags. All qualified samples were digested by enzymes, respectively (Zhang et al, 2022 ). The obtained enzyme SLAF tags were treated by adding one A at the 3′ end, and ligating a dual‐index sequencing connector (Kozich et al, 2013 ; Zhang et al, 2022 ), PCR amplification, purification, sample mixing, and gel cutting to select the target fragment.…”

Section: Methodsmentioning

confidence: 99%

“…All qualified samples were digested by enzymes, respectively (Zhang et al, 2022 ). The obtained enzyme SLAF tags were treated by adding one A at the 3′ end, and ligating a dual‐index sequencing connector (Kozich et al, 2013 ; Zhang et al, 2022 ), PCR amplification, purification, sample mixing, and gel cutting to select the target fragment. SLAF tags of 464–494 bp were gel‐purified for sequencing.…”

Section: Methodsmentioning

confidence: 99%

“…Population structure analysis was performed using the ADMIXTURE 1.3.0 (Alexander et al, 2009 ) based on the maximum likelihood method and K ranging from 1 to 10 while running ADMIXTURE five times to gauge convergence (Alexander et al, 2009 ). The cross‐validation error rate of K value was analyzed (Zhang et al, 2022 ). Using EIGENSOFT 3.0 software, principal component analysis (PCA) was carried out (Patterson et al, 2006 ).…”

Section: Methodsmentioning

confidence: 99%

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Molecular genetics and quantitative traits divergence among populations of Eothenomys miletus from Hengduan Mountain region

Ren

Jia

Cai

et al. 2023

Ecology and Evolution

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An important objective of evolutionary biology has always been to grasp the evolutionary and genetic processes that contribute to speciation. The present work provides the first detailed account of the genetic and physiological adaptation to changing environmental temperatures as well as the reasons causing intraspecific divergence in the Eothenomys miletus from the Hengduan Mountain (HM) region, one of the biodiversity hotspots. One hundred sixty‐one E. miletus individuals from five populations in the HM region had their reduced‐representation genome sequenced, and one additional individual from each community had their genomes resequenced. We then characterized the genetic diversity and population structure of each population and compared the phenotypic divergence in traits using neutral molecular markers. We detected significant phenotypic and genetic alterations in E. miletus from the HM region that were related to naturally occurring diverse habitats by combining morphometrics and genomic techniques. There was asymmetric gene flow among the E. miletus populations, indicating that five E. miletus populations exhibit an isolation‐by‐island model, and this was supported by the correlation between FST and geographic distance. Finally, PST estimated by phenotypic measures of most wild traits were higher than differentiation at neutral molecular markers, indicating directional natural selection favoring different phenotypes in different populations must have been involved to achieve this much differentiation. Our findings give information on the demographic history of E. miletus, new insights into their evolution and adaptability, and literature for studies of a similar nature on other wild small mammals from the HM region.

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“…In summary, the use of DNA molecular markers, particularly SNPs, for the identification of germplasm resources is crucial for overcoming the limitations of traditional morphological identification methods. DNA fingerprinting is a powerful method for identifying genetic diversity and distinguishing between different plant varieties based on molecular markers or specific sequences [30][31][32], which has been widely applied in the diversity assessment and purity identification of various crops [33].…”

Section: Introductionmentioning

confidence: 99%

Evaluation of Genetic Diversity and Agronomic Traits of Germplasm Resources of Stropharia rugosoannulata

Gu,

Chen,

Zhang

et al. 2024

Horticulturae

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China possesses abundant wild germplasm resources and a wide range of cultivated strains of Stropharia rugosoannulata. However, issues such as genetic diversity and unclear genetic relationships have had an impact on the classification and preservation of germplasm resources, the breeding of new varieties, and the promotion of superior strains. There is an urgent need for genetic diversity analysis and assessment of germplasm resources. In this study, we conducted whole-genome resequencing of 50 cultivated and wild strains collected from various regions across the country. After applying a series of filtering parameters, we obtained 888,536 high-quality Single Nucleotide Polymorphism (SNP) markers. Using these SNP markers, we performed principal component analysis, population structure analysis, and phylogenetic clusters analysis on the 50 strains. Most cultivated strains exhibited high genetic similarity, while significant genetic diversity was observed among wild strains. Based on factors such as marker distribution throughout the entire genome and marker quality, we selected 358 core SNP markers to construct SNP fingerprints. Two-dimensional barcodes were generated for each strain to enable specific identification. Additionally, the mycelial growth rate of strains was evaluated on Potato Dextrose Agar (PDA) and substrate culture media. We also assessed their lignin degradation capability using guaiacol agar plates assay. It was observed that the mycelial growth rate on PDA and substrate culture medium exhibited a significant correlation with the diameter of the mycelial colony on guaiacol agar medium. Additionally, the correlation between the mycelial growth rate on the substrate medium and that on the guaiacol agar plate was stronger than that on PDA medium. This study provided molecular-level identification and assessment of germplasm resources. It clarified the genetic relationships among strains and the characteristics of mycelium growth-related agronomic traits of each strain. This research contributed to the enrichment and development of utilizable germplasm resources and breeding materials for S. rugosoannulata, offering a scientific basis for further research.

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Development of SLAF-Sequence and Multiplex SNaPshot Panels for Population Genetic Diversity Analysis and Construction of DNA Fingerprints for Sugarcane

Cited by 11 publications

References 61 publications

Evaluation of a Sugarcane (Saccharum spp.) Hybrid F1 Population Phenotypic Diversity and Construction of a Rapid Sucrose Yield Estimation Model for Breeding

Evaluation of a Sugarcane (Saccharum spp.) Hybrid F1 Population Phenotypic Diversity and Construction of a Rapid Sucrose Yield Estimation Model for Breeding

Molecular genetics and quantitative traits divergence among populations of Eothenomys miletus from Hengduan Mountain region

Evaluation of Genetic Diversity and Agronomic Traits of Germplasm Resources of Stropharia rugosoannulata

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