Detection of Candidate Gene LsACOS5 and Development of InDel Marker for Male Sterility by DdRAD-Seq and Whole-Genome Sequencing in Lettuce (Lactuca Sativa L.)

Mapping Intimacies ◽

10.21203/rs.3.rs-1111028/v1 ◽

2021 ◽

Author(s):

kousuke seki

Keyword(s):

Candidate Gene ◽

Whole Genome Sequencing ◽

Male Sterility ◽

Genome Sequencing ◽

Indel Marker ◽

Hybrid Breeding ◽

Whole Genome ◽

Structural Polymorphism ◽

Male Sterile ◽

Breeding Method

Abstract A new breeding method of F1 hybrid using male sterility would open an exciting frontier in lettuce breeding, a self-pollinating crop. Male sterility is a crucial trait in F1 hybrid breeding. It is essential to map the causative gene for using male sterility. The ms-S, male-sterile gene of ‘CGN17397’, was mapped to LG8 by double-digest restriction site-associated DNA sequencing (ddRAD-seq) and narrowed down between two markers using two F2 populations. This region spans approximately 10.16 Mb, where 94 genes were annotated according to the lettuce reference genome sequence (version8 from crisphead cultivar ‘Salinas’). The whole-genome sequencing of the male-sterile and fertile lines of ‘CGN17397’ revealed that only one gene differed in the area of Lsat_1_v5_gn_8_148221.1, a homolog of Arabidopsis acyl-CoA synthetase5 (AtACOS5), and was deleted in the male-sterile lines. It was reported that AtACOS5 was needed for pollen wall formation and that the null mutants of AtACOS5 were entirely male sterility. Thus, I concluded that Lsat_1_v5_gn_8_148221.1 designated as LsACOS5 was a biologically plausible candidate gene for the ms-S locus. By using the structural polymorphism of LsACOS5, an insertion/deletion (InDel) marker was developed to select the male-sterile trait. The results obtained here provide valuable information for the genic male-sterility in lettuce.

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A Missense Mutation in the KLF7 Gene Is a Potential Candidate Variant for Congenital Deafness in Australian Stumpy Tail Cattle Dogs

Genes ◽

10.3390/genes12040467 ◽

2021 ◽

Vol 12 (4) ◽

pp. 467

Author(s):

Fangzheng Xu ◽

Shuwen Shan ◽

Susan Sommerlad ◽

Jennifer M. Seddon ◽

Bertram Brenig

Keyword(s):

Candidate Gene ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Heart Development ◽

Genome Wide Association Study ◽

Whole Genome ◽

Potential Candidate ◽

Congenital Deafness ◽

Cardiovascular Development ◽

A Genome

Congenital deafness is prevalent among modern dog breeds, including Australian Stumpy Tail Cattle Dogs (ASCD). However, in ASCD, no causative gene has been identified so far. Therefore, we performed a genome-wide association study (GWAS) and whole genome sequencing (WGS) of affected and normal individuals. For GWAS, 3 bilateral deaf ASCDs, 43 herding dogs, and one unaffected ASCD were used, resulting in 13 significantly associated loci on 6 chromosomes, i.e., CFA3, 8, 17, 23, 28, and 37. CFA37 harbored a region with the most significant association (−log10(9.54 × 10−21) = 20.02) as well as 7 of the 13 associated loci. For whole genome sequencing, the same three affected ASCDs and one unaffected ASCD were used. The WGS data were compared with 722 canine controls and filtered for protein coding and non-synonymous variants, resulting in four missense variants present only in the affected dogs. Using effect prediction tools, two variants remained with predicted deleterious effects within the Heart development protein with EGF like domains 1 (HEG1) gene (NC_006615.3: g.28028412G>C; XP_022269716.1: p.His531Asp) and Kruppel-like factor 7 (KLF7) gene (NC_006619.3: g.15562684G>A; XP_022270984.1: p.Leu173Phe). Due to its function as a regulator in heart and vessel formation and cardiovascular development, HEG1 was excluded as a candidate gene. On the other hand, KLF7 plays a crucial role in the nervous system, is expressed in the otic placode, and is reported to be involved in inner ear development. 55 additional ASCD samples (28 deaf and 27 normal hearing dogs) were genotyped for the KLF7 variant, and the variant remained significantly associated with deafness in ASCD (p = 0.014). Furthermore, 24 dogs with heterozygous or homozygous mutations were detected, including 18 deaf dogs. The penetrance was calculated to be 0.75, which is in agreement with previous reports. In conclusion, KLF7 is a promising candidate gene causative for ASCD deafness.

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Whole Genome Sequencing of Giant Schnauzer Dogs with Progressive Retinal Atrophy Establishes NECAP1 as a Novel Candidate Gene for Retinal Degeneration

Genes ◽

10.3390/genes10050385 ◽

2019 ◽

Vol 10 (5) ◽

pp. 385 ◽

Cited By ~ 3

Author(s):

Rebekkah J. Hitti ◽

James A. C. Oliver ◽

Ellen C. Schofield ◽

Anina Bauer ◽

Maria Kaukonen ◽

...

Keyword(s):

Candidate Gene ◽

Whole Genome Sequencing ◽

Retinal Degeneration ◽

Genome Sequencing ◽

Autosomal Recessive Disorder ◽

Causal Variant ◽

Whole Genome ◽

Gene Encoding ◽

Progressive Retinal Atrophy ◽

Dna Test

Canine progressive retinal atrophies (PRA) are genetically heterogeneous diseases characterized by retinal degeneration and subsequent blindness. PRAs are untreatable and affect multiple dog breeds, significantly impacting welfare. Three out of seven Giant Schnauzer (GS) littermates presented with PRA around four years of age. We sought to identify the causal variant to improve our understanding of the aetiology of this form of PRA and to enable development of a DNA test. Whole genome sequencing of two PRA-affected full-siblings and both unaffected parents was performed. Variants were filtered based on those segregating appropriately for an autosomal recessive disorder and predicted to be deleterious. Successive filtering against 568 canine genomes identified a single nucleotide variant in the gene encoding NECAP endocytosis associated 1 (NECAP1): c.544G>A (p.Gly182Arg). Five thousand one hundred and thirty canids of 175 breeds, 10 cross-breeds and 3 wolves were genotyped for c.544G>A. Only the three PRA-affected GS were homozygous (allele frequency in GS, excluding proband family = 0.015). In addition, we identified heterozygotes belonging to Spitz and Dachshund varieties, demonstrating c.544G>A segregates in other breeds of German origin. This study, in parallel with the known retinal expression and role of NECAP1 in clathrin mediated endocytosis (CME) in synapses, presents NECAP1 as a novel candidate gene for retinal degeneration in dogs and other species.

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