Quantitative Trait Loci Mapping and Development of KASP Marker Smut Screening Assay Using High-Density Genetic Map and Bulked Segregant RNA Sequencing in Sugarcane (Saccharum spp.)

Gao, Yurong; Zhou, Shan; Huang, Yuxin; Zhang, Baoqing; Xu, Yuhui; Zhang, Gemin; Lakshmanan, Prakash; Yang, Rei‐Cheng; Zhou, Hui; Huang, Dali; Liu, Junxian; Tan, Huachun; He, Weiming; Yang, Cuifang; WeiXing, Duan

doi:10.3389/fpls.2021.796189

Cited by 9 publications

(6 citation statements)

References 70 publications

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“…However, only limited research has been reported till now, including disease characteristics, control measures, and the isolation and identification of this pathogen [ 1 ]. With the rapid development of high-throughput sequencing and biotechnology in recent years, the BSR-seq technique has been widely used to quickly locate and screen genes related to target traits in various crops, such as maize [ 32 ], wheat [ 33 ], kiwifruit [ 10 ], and sugarcane [ 34 , 35 ]. Zhu et al [ 36 ] screened six candidate genes associated with wheat powdery mildew in wheat via BSR-seq.…”

Section: Discussionmentioning

confidence: 99%

Screening of Candidate Genes Associated with Brown Stripe Resistance in Sugarcane via BSR-seq Analysis

Cheng

Wang

et al. 2022

IJMS

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Sugarcane brown stripe (SBS), caused by the fungal pathogen Helminthosporium stenospilum, is one of the most serious threats to sugarcane production. However, its outbreaks and epidemics require suitable climatic conditions, resulting in the inefficient improvement of the SBS resistance by phenotype selection. The sugarcane F1 population of SBS-resistant YT93-159 × SBS-susceptible ROC22 was used for constructing the bulks. Bulked segregant RNA-seq (BSR-seq) was then performed on the parents YT93-159 (T01) and ROC22 (T02), and the opposite bulks of 30 SBS-susceptible individuals mixed bulk (T03) and 30 SBS-resistant individuals mixed bulk (T04) collected from 287 F1 individuals. A total of 170.00 Gb of clean data containing 297,921 SNPs and 70,426 genes were obtained. Differentially expressed genes (DEGs) analysis suggested that 7787 and 5911 DEGs were identified in the parents (T01 vs. T02) and two mixed bulks (T03 vs. T04), respectively. In addition, 25,363 high-quality and credible SNPs were obtained using the genome analysis toolkit GATK for SNP calling. Subsequently, six candidate regions with a total length of 8.72 Mb, which were located in the chromosomes 4B and 7C of sugarcane wild species Saccharum spontaneum, were identified, and 279 genes associated with SBS-resistance were annotated by ED algorithm and ΔSNP-index. Furthermore, the expression profiles of candidate genes were verified by quantitative real-time PCR (qRT-PCR) analysis, and the results showed that eight genes (LRR-RLK, DHAR1, WRKY7, RLK1, BLH4, AK3, CRK34, and NDA2) and seven genes (WRKY31, CIPK2, CKA1, CDPK6, PFK4, CBL2, and PR2) of the 20 tested genes were significantly up-regulated in YT93-159 and ROC22, respectively. Finally, a potential molecular mechanism of sugarcane response to H. stenospilum infection is illustrate that the activations of ROS signaling, MAPK cascade signaling, Ca2+ signaling, ABA signaling, and the ASA-GSH cycle jointly promote the SBS resistance in sugarcane. This study provides abundant gene resources for the SBS resistance breeding in sugarcane.

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Section: Discussionmentioning

confidence: 99%

Screening of Candidate Genes Associated with Brown Stripe Resistance in Sugarcane via BSR-seq Analysis

Cheng

Wang

et al. 2022

IJMS

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“…SNPs, being the most abundant and stable type of genetic marker, have been extensively generated through whole-genome resequencing [ 24 ] and various genome complexity-reduction protocols, including genotyping-by-sequencing [ 25 ], restriction site-associated DNA sequencing [ 26 ], and specific-length amplified fragment sequencing (SLAF-seq) [ 27 ]. SLAF-seq has been widely applied in many plants for various aspects of genetic/genomic research, including phylogenetic analysis [ 28 ], genome-wide association studies [ 29 ], high-density genetic map construction [ 30 ], and QTL mapping [ 31 ]. SLAF-seq is a valuable tool with the advantages of low cost and high throughput, particularly when plants or animals lack a reference genome.…”

Section: Introductionmentioning

confidence: 99%

Assessment of phylogenetic relationships and genetic diversity of Sagittaria trifolia using phenotypic traits and SNP markers

Ji,

Li,

Huang

et al. 2024

PLoS ONE

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The aquatic perennial herb Sagittaria trifolia L. commonly known as arrowhead, has been utilized in China both as a culinary vegetable and in traditional medicines. Characterizing the phylogenetic relationships and genetic diversity of arrowheads is crucial for improved management, conservation, and efficient utilization of the germplasm resources associated with this species. Herein, we presented the phenotypic traits and genome-wide DNA marker-based analyses of 111 arrowhead accessions, most of which were from China. Cluster analysis revealed that arrowhead could be categorized into two clusters based on 11 phenotypic traits, with Cluster 1 comprising two subclusters. All accessions were clustered into three sub-clusters based primarily on leaf shape and tuber weight. A set of 759,237 high-quality single-nucleotide polymorphisms was identified and used to assess the phylogenetic relationships. Population structure and phylogenetic tree analyses suggested that the accessions could be classified into two major groups, Group I was further subdivided into two subgroups, aligning with the clusters identified through morphological classification. By employing Sagittaria lichuanensis as an outgroup, the rooted tree revealed that the evolutionary relationships within the three groups followed a progression from Group I-1 to Group I-2 and finally to Group II. The landraces were clustered into one group along with the remaining wild accessions. The level of genetic diversity for Group I (π = 0.26) was slightly lower than that which was estimated for Group II (π = 0.29). The lowest pairwise differentiation levels (Fst, 0.008) were obtained from the comparison between groups I-2 and II, indicating that the two groups were the most closely related. This study provides novel insights into germplasm classification, evolutionary relationships, genomics and arrowhead breeding.

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“…However, these reported SNPs need to be validated for the linked traits to use them as molecular markers for MAS. To facilitate their use for MAS in sugarcane breeding, some of the trait-linked SNPs have been converted into allele-specific polymerase chain reaction assays ( Gao et al, 2022 ). These SNP markers are valuable tools for marker-assisted sugarcane breeding.…”

Section: Introductionmentioning

confidence: 99%

A SNP variation in the Sucrose synthase (SoSUS) gene associated with sugar-related traits in sugarcane

Khanbo,

Somyong,

Phetchawang

et al. 2023

PeerJ

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Background Sugarcane (Saccharum spp.) is an economically significant crop for both the sugar and biofuel industries. Breeding sugarcane cultivars with high-performance agronomic traits is the most effective approach for meeting the rising demand for sugar and biofuels. Molecular markers associated with relevant agronomic traits could drastically reduce the time and resources required to develop new sugarcane varieties. Previous sugarcane candidate gene association analyses have found single nucleotide polymorphism (SNP) markers associated with sugar-related traits. This study aims to validate these associated SNP markers of six genes, including Lesion simulating disease 1 (LSD), Calreticulin (CALR), Sucrose synthase 1 (SUS1), DEAD-box ATP-dependent RNA helicase (RH), KANADI1 (KAN1), and Sodium/hydrogen exchanger 7 (NHX7), in a diverse population in 2-year and two-location evaluations. Methods After genotyping of seven targeted SNP markers was performed by PCR Allelic Competitive Extension (PACE) SNP genotyping, the association with sugar-related traits and important cane yield component traits was determined on a set of 159 sugarcane genotypes. The marker-trait relationships were validated and identified by both t-test analysis and an association analysis based on the general linear model. Results The mSoSUS1_SNPCh10.T/C and mSoKAN1_SNPCh7.T/C markers that were designed from the SUS1 and KAN1 genes, respectively, showed significant associations with different amounts of sugar-related traits and yield components. The mSoSUS1_SNPCh10.T/C marker was found to have more significant association with sugar-related traits, including pol, CCS, brix, fiber and sugar yield, with p values of 6.08 × 10−6 to 4.35 × 10−2, as well as some cane yield component traits with p values of 1.61 × 10−4 to 3.35 × 10−2. The significant association is consistent across four environments. Conclusion Sucrose synthase (SUS) is considered a crucial enzyme involved in sucrose metabolism. This marker is a high potential functional marker that may be used in sugarcane breeding programs to select superior sugarcane with good fiber and high sugar contents.

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Quantitative Trait Loci Mapping and Development of KASP Marker Smut Screening Assay Using High-Density Genetic Map and Bulked Segregant RNA Sequencing in Sugarcane (Saccharum spp.)

Cited by 9 publications

References 70 publications

Screening of Candidate Genes Associated with Brown Stripe Resistance in Sugarcane via BSR-seq Analysis

Screening of Candidate Genes Associated with Brown Stripe Resistance in Sugarcane via BSR-seq Analysis

Assessment of phylogenetic relationships and genetic diversity of Sagittaria trifolia using phenotypic traits and SNP markers

A SNP variation in the Sucrose synthase (SoSUS) gene associated with sugar-related traits in sugarcane

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