Investigation of genetic relationships within three Miscanthus species using SNP markers identified with SLAF-seq

Chen, Zhiyong; He, Yancen; Iqbal, Yasir; Shí, Yùzhēn; Huang, Hongmei; Yi, Zili

doi:10.1186/s12864-021-08277-8

Cited by 9 publications

(7 citation statements)

References 53 publications

(65 reference statements)

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“…SLAFseq methods, however, are not the same as GBS methods in a few respects. For example, one tag is identified by SLAF-seq roughly every 10 K, the uniform distribution of SLAF tags guarantees that significant chromosomal segments are not overlooked, and SLAFseq is a cost-effective method since it avoids repeating sequences (Chen et al, 2022b). While both SLAF-seq and WGS can identify SNPs, they greatly differ in terms of cost-effectiveness and missing data.…”

Section: Discussionmentioning

confidence: 99%

Genome-wide survey reveals the genetic background of Xinjiang Brown cattle in China

Wang,

Ma,

Gao

et al. 2024

Front. Genet.

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Introduction: Xinjiang Brown cattle are a famous dual-purpose (dairy-beef) cultivated breed in China that occupy a pivotal position within the cattle breeding industry in Xinjiang, China. However, little information is available on the genetic background of this breed. To fill this research gap, we conducted a whole-genome screen using specific-locus amplified fragment sequencing to examine the genetic structure and diversity of 130 Xinjiang Brown cattle-grazing type (XBG, traditional type) cattle.Methods: A subsequent joint analysis incorporating two ancestral breeds, specifically 19 Brown Swiss (BS) foreign and nine Kazakh (KZ) Chinese cattle, as well as 20 Xinjiang Brown cattle-housing type (XBH) cattle, was used to explore the genetic background of the Xinjiang Brown cattle.Results: The results showed that, after nearly a century of crossbreeding, XBG cattle formed a single population with a stable genetic performance. The genetic structure, genetic diversity, and selection signature analysis of the two ancestral types showed highly different results compared to that of XBH cattle. Local ancestry inference showed that the average proportions of XGB cattle within the BS and KZ cattle lineages were 37.22% and 62.78%, respectively, whereas the average proportions of XBH cattle within the BS and KZ cattle lineages were 95.14% and 4.86%, respectively. Thus, XGB cattle are more representative of all Xinjiang Brown cattle, in line with their breeding history, which involves crossbreeding. Two complementary approaches, fixation index and mean nucleotide diversity, were used to detect selection signals in the four aforementioned cattle breeds. Finally, the analysis of 26 candidate genes in Xinjiang Brown cattle revealed significant enrichment in 19 Gene Ontology terms, and seven candidate genes were enriched in three pathways related to disease resistance (CDH4, SIRPB1, and SIRPα) and the endocrine system (ADCY5, ABCC8, KCNJ11, and KCNMA1). Finally, development of the core SNPs in XBG cattle yielded 8,379 loci.Conclusion: The results of this study detail the evolutionary process of crossbreeding in Xinjiang Brown cattle and provide guidance for selecting and breeding new strains of this species.

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Section: Discussionmentioning

confidence: 99%

Genome-wide survey reveals the genetic background of Xinjiang Brown cattle in China

Wang,

Ma,

Gao

et al. 2024

Front. Genet.

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“…In earlier times, conventional breeding methods encouraged plant growth under water stressed environments. These methods are very time-consuming and costly, and therefore the development of molecular markers played a crucial role in detecting the genetic variability in crops ( Chen et al, 2022 ). Many QTLs have been detected in many crops, but their reliability and accuracy are often problematic ( Xu et al, 2022 ).…”

Section: Molecular Techniques To Enhance Drought Tolerance In Ramiementioning

confidence: 99%

Improving Drought Stress Tolerance in Ramie (Boehmeria nivea L.) Using Molecular Techniques

Rasheed

Jie²,

Nawaz³

et al. 2022

Front. Plant Sci.

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Ramie is one of the most significant fiber crops and contributes to good quality fiber. Drought stress (DS) is one of the most devastating abiotic factors which is accountable for a substantial loss in crop growth and production and disturbing sustainable crop production. DS impairs growth, plant water relation, and nutrient uptake. Ramie has evolved a series of defense responses to cope with DS. There are numerous genes regulating the drought tolerance (DT) mechanism in ramie. The morphological and physiological mechanism of DT is well-studied; however, modified methods would be more effective. The use of novel genome editing tools like clustered regularly interspaced short palindromic repeats (CRISPR) is being used to edit the recessive genes in crops to modify their function. The transgenic approaches are used to develop several drought-tolerant varieties in ramie, and further identification of tolerant genes is needed for an effective breeding plan. Quantitative trait loci (QTLs) mapping, transcription factors (TFs) and speed breeding are highly studied techniques, and these would lead to the development of drought-resilient ramie cultivars. The use of hormones in enhancing crop growth and development under water scarcity circumstances is critical; however, using different concentrations and testing genotypes in changing environments would be helpful to sort the tolerant genotypes. Since plants use various ways to counter DS, investigating mechanisms of DT in plants will lead to improved DT in ramie. This critical review summarized the recent advancements on DT in ramie using novel molecular techniques. This information would help ramie breeders to conduct research studies and develop drought tolerant ramie cultivars.

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“…Over time, various types of molecular markers have been developed, encompassing the first-generation markers such as restriction fragment length polymorphism (RFLP), random amplified polymorphic DNA (RAPD), and amplified fragment length polymorphism (AFLP), as well as the second-generation markers like simple sequence repeats (SSR) and inter-simple sequence repeats (ISSR). Nonetheless, these markers exhibit limitations in terms of throughput, accuracy, time consumption, labor intensiveness, and cost ( Zheng et al., 2018 ; Clifton-brown et al., 2019 ; Chen et al., 2022 ). To surmount these challenges, a third generation of molecular markers known as SNPs has emerged.…”

Section: Introductionmentioning

confidence: 99%

Identification of molecular markers and candidate regions associated with grain number per spike in Pubing3228 using SLAF-BSA

Wang,

Cheng

et al. 2024

Front. Plant Sci.

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Grain number per spike, a pivotal agronomic trait dictating wheat yield, lacks a comprehensive understanding of its underlying mechanism in Pubing3228, despite the identification of certain pertinent genes. Thus, our investigation sought to ascertain molecular markers and candidate regions associated with grain number per spike through a high-density genetic mapping approach that amalgamates site-specific amplified fragment sequencing (SLAF-seq) and bulked segregation analysis (BSA). To facilitate this, we conducted a comparative analysis of two wheat germplasms, Pubing3228 and Jing4839, known to exhibit marked discrepancies in spike shape. By leveraging this methodology, we successfully procured 2,810,474 SLAF tags, subsequently resulting in the identification of 187,489 single nucleotide polymorphisms (SNPs) between the parental strains. We subsequently employed the SNP-index association algorithm alongside the extended distribution (ED) association algorithm to detect regions associated with the trait. The former algorithm identified 24 trait-associated regions, whereas the latter yielded 70. Remarkably, the intersection of these two algorithms led to the identification of 25 trait-associated regions. Amongst these regions, we identified 399 annotated genes, including three genes harboring non-synonymous mutant SNP loci. Notably, the APETALA2 (AP2) transcription factor families, which exhibited a strong correlation with spike type, were also annotated. Given these findings, it is plausible to hypothesize that these genes play a critical role in determining spike shape. In summation, our study contributes significant insights into the genetic foundation of grain number per spike. The molecular markers and candidate regions we have identified can be readily employed for marker-assisted breeding endeavors, ultimately leading to the development of novel wheat cultivars possessing enhanced yield potential. Furthermore, conducting further functional analyses on the identified genes will undoubtedly facilitate a comprehensive elucidation of the underlying mechanisms governing spike development in wheat.

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Investigation of genetic relationships within three Miscanthus species using SNP markers identified with SLAF-seq

Cited by 9 publications

References 53 publications

Genome-wide survey reveals the genetic background of Xinjiang Brown cattle in China

Genome-wide survey reveals the genetic background of Xinjiang Brown cattle in China

Improving Drought Stress Tolerance in Ramie (Boehmeria nivea L.) Using Molecular Techniques

Identification of molecular markers and candidate regions associated with grain number per spike in Pubing3228 using SLAF-BSA

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