Genomic insight into the developmental history of southern highbush blueberry populations

ハイブッシュブルーベリーに暖地適応性をもたらした遺伝要因を解明 --ゲノムに刻まれたブルーベリーの育種履歴--. 京都大学プレスリリース. 2020-09-07.Interspecific hybridization is a common breeding approach for introducing novel traits and genetic diversity to breeding populations. Southern highbush blueberry (SHB) is a blueberry cultivar group that has been intensively bred over the last 60 years. Specifically, it was developed by multiple interspecific crosses between northern highbush blueberry [NHB, Vaccinium corymbosum L. (2n = 4x = 48)] and low-chill Vaccinium species to expand the geographic limits of highbush blueberry production. In this study, we genotyped polyploid blueberries, including 105 SHB, 17 NHB, and 10 rabbiteye blueberry (RE) (Vaccinium virgatum Aiton), from the accessions planted at Poplarville, Mississippi, and accessions distributed in Japan, based on the double-digest restriction site-associated DNA sequencing. The genome-wide SNP data clearly indicated that RE cultivars were genetically distinct from SHB and NHB cultivars, whereas NHB and SHB were genetically indistinguishable. The population structure results appeared to reflect the differences in the allele selection strategies that breeders used for developing germplasm adapted to local climates. The genotype data implied that there are no or very few genomic segments that were commonly introgressed from low-chill Vaccinium species to the SHB genome. Principal component analysis-based outlier detection analysis found a few loci associated with a variable that could partially differentiate NHB and SHB. These SNP loci were detected in Mb-scale haplotype blocks and may be close to the functional genes related to SHB development. Collectively, the data generated in this study suggest a polygenic adaptation of SHB to the southern climate, and may be relevant for future population-scale genome-wide analyses of blueberry

Functional and expressional analyses of apple FLC-like in relation to dormancy progress and flower bud development.

We previously identified the FLOWERING LOCUS C (FLC)-like gene, a MADS-box transcription factor gene that belongs to Arabidopsis thaliana L. FLC clade, in apple (Malus ×domestica Borkh.), and its expression in dormant flower buds is positively correlated with cumulative cold exposure. To elucidate the role of the MdFLC-like in the dormancy process and flower development, we first characterized the phenotypes of MdFLC-like overexpressing lines with the Arabidopsis Columbia-0 background. The overexpression of MdFLC-like significantly delayed the bolting date and reduced the plant size, but it did not significantly affect the number of rosette leaves or flower organ formation. Thus, MdFLC-like may affect vegetative growth and development rather than flowering when expressed in Arabidopsis, which is not like Arabidopsis FLC that affects development of flowering. We compared seasonal expression patterns of MdFLC-like in low-chill ‘Anna’ and high-chill ‘Fuji’ and ‘Tsugaru’ apples collected from trees grown in a cold winter region in temperate zone and found an earlier upregulation in ‘Anna’ compared with ‘Fuji’ and ‘Tsugaru’. Expression patterns were also compared in relation to developmental changes in the flower primordia during the chilling accumulation period. Overall, MdFLC-like was progressively upregulated during flower primordia differentiation and development in autumn to early winter and reached a maximum expression level at around the same time as the genotype-dependent chilling requirements were fulfilled in high-chill cultivars. Thus, we hypothesize MdFLC-like may be upregulated in response to cold exposure and flower primordia development during the progress of endodormancy. Our study also suggests MdFLC-like may have a growth-inhibiting function during the end of endodormancy and ecodormancy when the temperature is low and unfavorable for rapid bud outgrowth

マメガキ(Diospyros lotus L.)における雌雄性判別分子マーカーの開発とカキ(D. kaki Thunb.)への適用

植物で初、雌雄異株性の性決定因子を柿において発見. 京都大学プレスリリース. 2014-10-31.Sexuality of crops affects both cultivation and breeding systems. Cultivated persimmon (Diospyros kaki Thunb) has a morphologically well-characterized polygamous or gyonodioecious sexual system. However, the genetic basis of sexuality in D. kaki has yet to be characterized. Here, we used dioecious D. lotus L., a diploid wild relative species to hexaploid or nonaploid D. kaki, as a model to clarify the genetic basis of sexuality in Diospyros and to develop molecular markers associated with the sexuality of individuals. Using 62 F1 offspring segregated into distinct male/female phenotypes, we found two amplified fragment-length polymorphism markers, DlSx-AF4 and DlSx-AF7, which cosegregated with maleness. This could suggest that the sexuality of D. lotus is controlled by a single gene/haploblock, and the male is dominant over the female. Thus, D. lotus’s sexuality can be described as the heterogametic male type, the XY-type, as reported for most other dioecious plant species. For unknown reasons, segregation of the phenotype of a sequence-characterized amplified region marker developed from DlSx-AF4 (DlSx-AF4S) and/or the male/female phenotype in two different crosses in D. lotus showed an apparent bias towards femaleness and better fitted 1:2 than 1:1, which is the theoretical segregation for a single genetic locus or haploblock in diploid D. lotus. DlSx-AF4S could distinguish D. kaki cultivars with female and male flowers from cultivars with only female flowers, strongly indicating that the same genetic system controls D. kaki’s sexuality and that DlSx-AF4S could be used as a genetic marker for sexuality in D. kaki breeding programs.雌雄性は作物の栽培そして育種の大きな制限要因となる．カキ（Diospyros kaki Thunb.）の雌雄性に関してこれまでに多くの形態学的な観察が行われ，カキは雌雄混株あるいは雌性両性異株とされている．しかしながら，カキにおける雌雄性の遺伝制御機構は明らかにされていない．本研究では，カキ（六倍体あるいは九倍体）の近縁野生種であり，雌雄異株であるマメガキ（D. lotus L.）（二倍体）を用い，交雑分離集団を作出し，雌雄分離の調査を行った．また同じ集団を用いて AFLP 解析によって雌雄性判別のための分子マーカーの開発を試みたところ，雄性と共分離を示す 2 種類の AFLP バンド（DlSx-AF4 および DlSx-AF7）が同定された．このため，マメガキの雌雄性は，他の多くの雌雄異株の植物種と同じく，単一の遺伝子座（ハプロブロック）によって支配される雄性異型接合型（XY 型）であることが明らかになった．しかし，DlSx-AF4 から作製した SCAR マーカー DlSx-AF4S および雌雄性形質の分離は，一遺伝子座支配における理論値である 1:1 から有意に雌性側に偏り，1:2 に近い分離を示した．DlSx-AF4S はカキにおいても雄花の着花性と相関を示し，カキの雌雄性もマメガキと同様の遺伝制御を受けていること，ならびにカキの育種における DlSx-AF4S を用いたマーカー選抜の可能性が示された

The objective function for the estimation of the differential coefficients of the -th gene's expression levels

<p><b>Copyright information:</b></p><p>Taken from "Function approximation approach to the inference of reduced NGnet models of genetic networks"</p><p>http://www.biomedcentral.com/1471-2105/9/23</p><p>BMC Bioinformatics 2008;9():23-23.</p><p>Published online 14 Jan 2008</p><p>PMCID:PMC2258286.</p><p></p

Violation of Emergent Rotational Symmetry in the Hexagonal Kagome Superconductor CsV₃Sb₅

This data file contains data presented in the titled paper

Quasi-two-dimensional Fermi surface of superconducting line-nodal metal CaSb2

We report on the Fermi surfaces and superconducting parameters of CaSb₂ single crystals (superconducting below Tc ~ 1.8 K) grown by the self-flux method. The frequency of de Haas–van Alphen and Shubnikov–de Haas oscillations evidences a quasi-two-dimensional (quasi-2D) Fermi surface, consistent with one of the Fermi surfaces forming Dirac lines predicted by first-principles calculations. Measurements in the superconducting state reveal that CaSb₂ is close to a type-I superconductor with the Ginzburg-Landau parameter of around unity. The temperature dependence of the upper critical field Hc₂ is well described by a model considering two superconducting bands, and the enhancement of the effective mass estimated from Hc₂(0K) is consistent with the quasi-2D band observed by the quantum oscillations. Our results indicate that a quasi-2D band forming Dirac lines contributes to the superconductivity in CaSb₂