Genetic Dissection of a Precocious Phenotype in Male Tiger Pufferfish (Takifugu rubripes) using Genotyping by Random Amplicon Sequencing, Direct (GRAS-Di)

A Survey of Genome-Wide Genetic Characterizations of Crossbred Dairy Cattle in Local Farms in Cambodia

Simple Summary

The Cambodian dairy sector collapsed due to the civil war. Thereby, the Cambodia dairy sector has not obtained basic information, such as cattle breed and milk production. To encourage the recovery of the Cambodian dairy sector, the present study aimed to reveal the genetic variation and the milk production in Cambodian crossbred dairy cattle. Initially, we conducted interviews to understand the breeding background and milk production of two local farms (Farm R and Farm M) in Cambodia. The percentage (%) of milk fat content in Farm R was higher than that in Farm M. A genome-wide analysis of the genetic characterization for 75 cows in the two dairy farms implies that some cows in Farm R are genetically far from other crossbred cattle and retain a higher proportion of genetic background derived from Cambodian-native cattle. The present study indicated genetic characteristics and milk composition in Cambodian crossbred cattle. Gene character in Cambodian local crossbred cattle could contribute to milk production in the Cambodian dairy system. Thus, our basic genetic study could provide a new breeding strategy by using local Cambodian crossbred dairy cattle to establish an adequate dairy strain.

Abstract

To improve the dairy sector in Cambodia in the future, we aimed to reveal the genetic variation and the milk production in Cambodian crossbred dairy cattle. We calculated the percent (%) milk fat content and the average milk yield per cow (L/day) for two farms (Farm R and M) based on the farmers’ records and interviews. The crossbred cows originated from Cambodian local farmers and Thailand breeders in Farm R, whereas the crossbred cows originated in Thailand breeders in Farm M. Then, we performed genetic characterization for 75 individuals from the two farms and an individual Japanese pure Holstein-Friesian cow based on 133,705 single nucleotide polymorphisms (SNPs) obtained by the GRAS-Di method. The milk fat contents in the bulk milk in the dry season and the average milk yield per cow on Farm R were 3.77 ± 0.98% and 7.81 ± 2.66 L/day, respectively, and were higher than those on Farm M (3.35 ± 0.54% and 6.5–7.5 L/day). Cattle originating in Cambodia in Farm R possessed a unique genetic character different from cattle from Thailand in Farm M. The present study suggests that the differences in milk fat content between the two farms might be explained by the genetic differences in crossbred cows.

Genetic basis of maturity time is independent from that of flowering time and contributes to ecotype differentiation in common buckwheat (Fagopyrum esculentum Moench)

BACKGROUND

Common buckwheat is considered a quantitative short-day plant and is classified into the autumn (highly photoperiod sensitive), summer (weakly photoperiod sensitive), and intermediate ecotype. Understanding ecotype differentiation is essential for adaptive expansion and maximizing yield. The genetic analysis for ecotype has focused on photoperiod-dependent flowering time, whereas post-flowering traits such as seed set and maturity time might also regulate ecotype differentiation.

RESULTS

A field experiment revealed that ecotype differentiation is mainly defined by the timing of seed set and maturation, whereas flowering time is less relevant. Thus, we focused on maturity time as a trait that defines the ecotype. To detect QTLs for maturity time, we developed two F₂ populations derived from early × late-maturing accessions and intermediate × late-maturing accessions. Using genotyping by random amplicon sequencing-direct analysis, we generated a high-density linkage map. QTL analysis detected two major QTLs for maturity time, one in each F₂ population. We also detected QTLs for flowering time at loci different from maturity time QTLs, which suggests that different genetic mechanisms regulate flowering and maturity. Association analysis showed that both QTLs for maturity time were significantly associated with variations in the trait across years.

CONCLUSIONS

Maturity time appeared to be more suitable for explaining ecotype differentiation than flowering time, and different genetic mechanisms would regulate the timing of flowering and maturation. The QTLs and QTL-linked markers for maturity time detected here may be useful to extend the cultivation area and to fine-tune the growth period to maximize yield in buckwheat.

MIG-seq is an effective method for high-throughput genotyping in wheat (Triticum spp.)

MIG-seq (Multiplexed inter-simple sequence repeats genotyping by sequencing) has been developed as a low cost genotyping technology, although the number of polymorphisms obtained is assumed to be minimal, resulting in the low application of this technique to analyses of agricultural plants. We applied MIG-seq to 12 plant species that include various crops and investigated the relationship between genome size and the number of bases that can be stably sequenced. The genome size and the number of loci, which can be sequenced by MIG-seq, are positively correlated. This is due to the linkage between genome size and the number of simple sequence repeats (SSRs) through the genome. The applicability of MIG-seq to population structure analysis, linkage mapping, and quantitative trait loci (QTL) analysis in wheat, which has a relatively large genome, was further evaluated. The results of population structure analysis for tetraploid wheat showed the differences among collection sites and subspecies, which agreed with previous findings. Additionally, in wheat biparental mapping populations, over 3,000 SNPs/indels with low deficiency were detected using MIG-seq, and the QTL analysis was able to detect recognized flowering-related genes. These results revealed the effectiveness of MIG-seq for genomic analysis of agricultural plants with large genomes, including wheat.

Genomic prediction for testes weight of the tiger pufferfish, Takifugu rubripes, using medium to low density SNPs

Aquaculture production is expected to increase with the help of genomic selection (GS). The possibility of performing GS using only a small number of SNPs has been examined in order to reduce genotyping costs; however, the practicality of this approach is still unclear. Here, we tested whether the effects of reducing the number of SNPs impaired the prediction accuracy of GS for standard length, body weight, and testes weight in the tiger pufferfish (Takifugu rubripes). High values for predictive ability (0.563-0.606) were obtained with 4000 SNPs for all traits under a genomic best linear unbiased predictor (GBLUP) model. These values were still within an acceptable range with 1200 SNPs (0.554-0.588). However, predictive abilities and prediction accuracies deteriorated using less than 1200 SNPs largely due to the reduced power in accurately estimating the genetic relationship among individuals; family structure could still be resolved with as few as 400 SNPs. This suggests that the SNPs informative for estimation of genetic relatedness among individuals differ from those for inference of family structure, and that non-random SNP selection based on the effects on family structure (e.g., site-F_ST, principal components, or random forest) is unlikely to increase the prediction accuracy for these traits.

Effect of Three Types of Ion Beam Irradiation on Gerbera (Gerbera hybrida) In Vitro Shoots with Mutagenesis Efficiency

Gerbera in vitro shoots were irradiated using three types of ion beams with different line energy transfers (LETs) to investigate the effective LET and absorbed doses for mutagenesis. Furthermore, genomic mutation analyses were conducted on the obtained mutants. Survival rate analysis showed a lower lethal dose 50% (LD₅₀) with ion beams with higher LETs. Trait/morphological mutations exhibited changes in the color and shape of petals and male sterility. Irradiation conditions with the highest growth change and trait/morphological mutation rates in each ion were C irradiation at 10 Gy, Ar irradiation at 5 Gy, and Fe irradiation at 5 Gy, with a range of absorbed dose of around LD₅₀ to about 10 Gy lower. The highest trait/morphological mutation rate was 14.1% with Ar irradiation at 5 Gy, which was one of the criteria for ion beam irradiation of gerbera in vitro shoots. Furthermore, the genomic mutation in the flower color, petal shape, and male sterile mutants were confirmed by genotype analysis using Genotyping by Random Amplicon Sequencing-Direct technology. This is the first study to report the efficient production of gerbera mutants that could be analyzed. Our findings may lead to more efficient gerbera mutant production and analysis technology.