scholarly journals Identification of Fruit Firmness QTL ff2.1 by SLAF-BSA and QTL Mapping in Melon

2021 ◽  
Author(s):  
Dongyang Dai ◽  
Shuang Zeng ◽  
Ling Wang ◽  
Junfeng Li ◽  
Peng Ji ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Bulked Segregant Analysis ◽  
Economic Value ◽  
Fruit Firmness ◽  
Melon Genome ◽  
Specific Locus ◽  
Parental Lines ◽  
Caps Markers ◽  
Significant Expression ◽  
Simple Sequence

Abstract Fruit firmness is an important target of melon breeding, as it is associated with shelf life and economic value; however, the precise mechanism determining fruit firmness during fruit ripening remains elusive. In the present study, one hundred forty-four F2 plants and F2-3 families derived from the high-firmness melon line M2-10 and the low-firmness melon line ZT091 were used to identify major quantitative trait loci (QTLs) by specific-locus amplified fragment (SLAF) sequencing with bulked segregant analysis (BSA). Simple sequence repeat (SSR) and cleaved amplified polymorphic sequence (Caps) markers based on the resequencing of parental lines were also used to narrow the associated region to identify candidate genes. Two regions associated with fruit firmness were investigated, including a 4.87 Mb region on chr. 2 and a 28.7 Mb region on chr. 5 of the melon genome. SSR and Caps markers were used to construct a genetic map of the associated regions: QTL ff5.1 was located between CmSSR13509 and CmSSR13423 and explained 38.44% of the observed variation, with an LOD threshold of 17.44; ff2.1 was located between CmSSR07709 and SNP22228 and explained 28.14% of the variation, with an LOD threshold of 3.8, and this region included 106 Kb and 10 candidate genes. Quantitative Real-time PCR (qRT-PCR) was used to investigated the investigate candidate gene expression at 15, 20 and 25 days after pollination (DAP) in the parental lines, and significant expression levels were detected for most of the genes, including four genes of unknown function and MELO3C017519, MELO3C017520, MELO3C017522, MELO3C029506, and MELO3C029520. These results revealed a new QTL, ff2.1, for melon fruit firmness-related gene identification.

Detection of polymorphic simple-sequence repeat markers that show linkage to a novel sugarcane brown rust disease resistance gene in resistant and susceptible genetic pools

2020 ◽  
pp. 1-7
Author(s):  
Jie Li ◽  
Xiao-Yan Wang ◽  
Hong-Li Shan ◽  
Rong-Yue Zhang ◽  
Chan-Mi Wang ◽  
...  
Keyword(s):  
Resistance Genes ◽  
Genetic Linkage ◽  
Genetic Linkage Map ◽  
Brown Rust ◽  
Cross Combination ◽  
Map Construction ◽  
Parental Lines ◽  
Genetic Pools ◽  
Simple Sequence ◽  
Rust Resistance Genes

Abstract Sugarcane brown rust, caused by Puccinia melanocephala, is one of the main diseases of sugarcane in China. The identification and discovery of new resistance genes have important theoretical and practical significance for preventing outbreaks of brown rust and ensuring the sustainable production of sugarcane. To screen for polymorphic simple-sequence repeat (SSR) molecular markers for localization of brown rust resistance genes, we used two populations that are suitable for genetic linkage map construction and mapping of new resistance genes to construct resistant and susceptible genetic pools. We then screened 449 pairs of primers to identify polymorphic SSR markers in the parental lines and the resistant/susceptible genetic pools. The results showed that 25 pairs of primers directed amplification of polymorphic DNA fragments between the parents of the cross combination ‘Yuetang 03-393’ × ‘ROC 24’, and 16 pairs of primers amplified polymorphic fragments between the parents of the cross combination ‘Liucheng 03-1137’ × ‘Dezhe 93-88’. Four pairs of primers (SMC236CG, SCESSR0928, SCESSR0636 and SCESSR2551) amplified polymorphic DNA fragments between the parental lines and the resistant/susceptible genetic pools in ‘Yuetang 03-393’ × ‘ROC 24’. The results of this study will establish a solid foundation for the mapping of new brown rust resistance genes, genetic linkage map construction and the development of closely-associated molecular markers in sugarcane.

scholarly journals Bulked segregant analysis reveals candidate genes responsible for dwarf formation in woody oilseed crop castor bean

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Zaiqing Wang ◽  
Anmin Yu ◽  
Fei Li ◽  
Wei Xu ◽  
Bing Han ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Castor Bean ◽  
Woody Plants ◽  
Molecular Mechanisms ◽  
Ricinus Communis ◽  
Bulked Segregant Analysis ◽  
Oilseed Crop ◽  
Yeast Transformation ◽  
Dwarf Phenotype ◽  
Genetic Breeding

AbstractPlant dwarfism is a desirable agronomic trait in non-timber trees, but little is known about the physiological and molecular mechanism underlying dwarfism in woody plants. Castor bean (Ricinus communis) is a typical woody oilseed crop. We performed cytological observations within xylem, phloem and cambia tissues, revealing that divergent cell growth in all tissues might play a role in the dwarf phenotype in cultivated castor bean. Based on bulked segregant analyses for a F2 population generated from the crossing of a tall and a dwarf accession, we identified two QTLs associated with plant height, covering 325 candidate genes. One of these, Rc5NG4-1 encoding a putative IAA transport protein localized in the tonoplast was functionally characterized. A non-synonymous SNP (altering the amino acid sequence from Y to C at position 218) differentiated the tall and dwarf plants and we confirmed, through heterologous yeast transformation, that the IAA uptake capacities of Rc5NG4-1Y and Rc5NG4-1C were significantly different. This study provides insights into the physiological and molecular mechanisms of dwarfing in woody non-timber economically important plants, with potential to aid in the genetic breeding of castor bean and other related crops.

scholarly journals A High-Density EST-SSR-Based Genetic Map and QTL Analysis of Dwarf Trait in Cucurbita pepo L.

2018 ◽  
Vol 19 (10) ◽  
pp. 3140 ◽  
Author(s):  
Chenggang Xiang ◽  
Ying Duan ◽  
Hongbo Li ◽  
Wei Ma ◽  
Sanwen Huang ◽  
...  
Keyword(s):  
Genetic Map ◽  
Simple Sequence Repeats ◽  
Cucurbita Pepo ◽  
Economic Value ◽  
High Density ◽  
Oxidase Gene ◽  
Phenotypic Polymorphism ◽  
The Rich ◽  
Expressed Sequence ◽  
Simple Sequence

As one of the earliest domesticated species, Cucurbita pepo (including squash and pumpkin) is rich in phenotypic polymorphism and has huge economic value. In this research, using 1660 expressed sequence tags-simple sequence repeats (EST-SSRs) and 632 genomic simple sequence repeats (gSSRs), we constructed the highest-density EST-SSR-based genetic map in Cucurbita genus, which spanned 2199.1 cM in total and harbored 623 loci distributed in 20 linkage groups. Using this map as a bridge, the two previous gSSR maps were integrated by common gSSRs and the corresponding relationships around chromosomes in three sets of genomes were also collated. Meanwhile, one large segmental inversion that existed between our map and the C. pepo genome was detected. Furthermore, three Quantitative Trait Loci (QTLs) of the dwarf trait (gibberellin-sensitive dwarf type) in C. pepo were located, and the candidate region that covered the major QTL spanned 1.39 Mb, which harbored a predicted gibberellin 2-β-oxidase gene. Considering the rich phenotypic polymorphism, the important economic value in the Cucurbita genus species and several advantages of the SSR marker were identified; thus, this high-density EST-SSR-based genetic map will be useful in Pumpkin and Squash breeding work in the future.

scholarly journals Identification of candidate genes controlling chilling tolerance of rice in the cold region at the booting stage by BSA-Seq and RNA-Seq

2020 ◽  
Vol 7 (11) ◽  
pp. 201081
Author(s):  
Zhenhua Guo ◽  
Lijun Cai ◽  
Zhiqiang Chen ◽  
Ruiying Wang ◽  
Lanming Zhang ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Bulked Segregant Analysis ◽  
Expression Patterns ◽  
Enrichment Analysis ◽  
Chilling Tolerance ◽  
Pathway Enrichment Analysis ◽  
Potential Candidate ◽  
Rice Varieties ◽  
Booting Stage ◽  
F2 Population

Rice is sensitive to low temperatures, specifically at the booting stage. Chilling tolerance of rice is a quantitative trait loci that is governed by multiple genes, and thus, its precise identification through the conventional methods is an arduous task. In this study, we investigated the candidate genes related to chilling tolerance at the booting stage of rice. The F2 population was derived from Longjing25 (chilling-tolerant) and Longjing11 (chilling-sensitive) cross. Two bulked segregant analysis pools were constructed. A 0.82 Mb region containing 98 annotated genes on chromosomes 6 and 9 was recognized as the candidate region associated with chilling tolerance of rice at the booting stage. Transcriptomic analysis of Longjing25 and Longjing11 revealed 50 differentially expressed genes (DEGs) on the candidate intervals. KEGG pathway enrichment analysis of DEGs was performed. Nine pathways were found to be enriched, which contained 10 DEGs. A total of four genes had different expression patterns or levels between Longjing25 and Longjing11. Four out of the 10 DEGs were considered as potential candidate genes for chilling tolerance. This study will assist in the cloning of the candidate genes responsible for chilling tolerance and molecular breeding of rice for the development of chilling-tolerant rice varieties.

scholarly journals Identification of a Major QTL (qRRs-10.1) That Confers Resistance to Ralstonia solanacearum in Pepper (Capsicum annuum) Using SLAF-BSA and QTL Mapping

2019 ◽  
Vol 20 (23) ◽  
pp. 5887 ◽  
Author(s):  
Heshan Du ◽  
Changlong Wen ◽  
Xiaofen Zhang ◽  
Xiulan Xu ◽  
Jingjing Yang ◽  
...  
Keyword(s):  
Qtl Mapping ◽  
Capsicum Annuum ◽  
Ralstonia Solanacearum ◽  
Bulked Segregant Analysis ◽  
Severity Index ◽  
Clear Cut ◽  
Close Proximity ◽  
Specific Locus ◽  
Resistance Markers ◽  
Resistant Rootstock

The soilborne pathogen Ralstonia solanacearum is the causal agent of bacterial wilt (BW), a major disease of pepper (Capsicum annuum). The genetic basis of resistance to this disease in pepper is not well known. This study aimed to identify BW resistance markers in pepper. Analysis of the dynamics of bioluminescent R. solanacearum colonization in reciprocal grafts of a resistant (BVRC 1) line and a susceptible (BVRC 25) line revealed that the resistant rootstock effectively suppressed the spreading of bacteria into the scion. The two clear-cut phenotypic distributions of the disease severity index in 440 F2 plants derived from BVRC 25 × BVRC 1 indicated that a major genetic factor as well as a few minor factors that control BW resistance. By specific-locus amplified fragment sequencing combined with bulked segregant analysis, two adjacent resistance-associated regions on chromosome 10 were identified. Quantitative trait (QTL) mapping revealed that these two regions belong to a single QTL, qRRs-10.1. The marker ID10-194305124, which reached a maximum log-likelihood value at 9.79 and accounted for 19.01% of the phenotypic variation, was located the closest to the QTL peak. A cluster of five predicted R genes and three defense-related genes, which are located in close proximity to the significant markers ID10-194305124 or ID10-196208712, are important candidate genes that may confer BW resistance in pepper.

Recent advances in understanding cotton fibre and seed development

2005 ◽  
Vol 15 (4) ◽  
pp. 269-280 ◽  
Author(s):  
Yong-Ling Ruan
Keyword(s):  
Candidate Genes ◽  
Cotton Seed ◽  
Economic Value ◽  
Cell System ◽  
Cotton Fibre ◽  
Cellulose Synthesis ◽  
Tetraploid Cotton ◽  
Cellular Processes ◽  
Fibre Development

The unique feature of the seed of tetraploid cotton (Gossypium hirsutum and Gossypium barbadense) is that about 30% of the seed coat epidermal cells develop into cellulose-enriched fibres, while the embryos synthesize oils and proteins. Hence, both the maternal and filial tissues of the cotton seed are of significant economic value. After initiation from the ovule epidermis at or just before anthesis, the single-celled fibres elongate to 2.5–6.0 cm long in the tetraploid species before they switch to intensive secondary cell wall cellulose synthesis. Thus, apart from its agronomic importance, the cotton fibre represents a model single-cell system to study the control of cell differentiation and elongation, carbon partitioning to cellulose synthesis and also the interaction between maternal (fibre) and embryonic tissues in seeds. Over the past decade or so, significant effort has been made to understand the cellular and molecular basis of cotton fibre development and oil biosynthesis in the embryo. Metabolic engineering of the oil biosynthetic pathway in cotton seed has successfully produced healthier and stable oils. A number of candidate genes and cellular processes that potentially regulate various aspects of fibre development have been identified. Further elucidation of the in vivo functions of those candidate genes could significantly deepen our understanding of fibre development and offer potential for improvement of fibre quality through genetic engineering or marker-assisted breeding approaches.

scholarly journals Genetic Analysis and Related Gene Primary Mapping of Heat Stress Tolerance in Cucumber Using Bulked Segregant Analysis

HortScience ◽  
2019 ◽  
Vol 54 (3) ◽  
pp. 423-428
Author(s):  
Min Wang ◽  
Wenrui Liu ◽  
Biao Jiang ◽  
Qingwu Peng ◽  
Xiaoming He ◽  
...  
Keyword(s):  
Heat Stress ◽  
Genetic Analysis ◽  
Candidate Genes ◽  
High Temperatures ◽  
Genomic Sequence ◽  
Bulked Segregant Analysis ◽  
Recessive Gene ◽  
Chromosome 1 ◽  
Isolation And Characterization ◽  
Indel Markers

Heat stress (HS) negatively influences plant development and growth, especially production and quality. Cucumber is a widely cultivated plant in the gourd family Cucurbitaceae that is often exposed to high temperatures during summer and protected cultivation. In this study, we performed whole-genome re-sequencing of two pools, one heat-tolerant and one heat-sensitive, of the F2 population derived from L-9 (heat-resistant) and A-16 (heat-sensitive). The genetic analysis showed that the heat resistance of L-9 cucumber seedlings was controlled by a single recessive gene. By combining bulked segregant analysis (BSA) technology, the crucial gene related to HS was preliminarily mapped to a 1.08-Mb region on chromosome 1. To fine-map the locus, Indel markers were designed according to the genomic sequence. Finally, the gene was narrowed to a 550-kb region flanked by two Indel markers, namely Indel-H90 and Indel-H224, that contained 56 candidate genes. Re-sequencing results indicated that 10 candidate genes among the 56 in the candidate region showed single base pair differences in the exons. Quantitative reverse-transcription polymerase chain reaction showed that 6 genes among the 10 candidate genes were significantly decreased when exposed to high temperatures. These results not only were useful for the isolation and characterization of the key genes involved in HS but also provided a basis for understanding the mechanism of heat tolerance regulation.

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