Functional Allele Research Articles

Deiodinase variation and liothyronine treatment interaction to accelerate ECT response in major depression: Pilot data and implications for thyroid pharmacogenomic testing in mood disorders

BackgroundConcurrent liothyronine treatment has been shown to accelerate time to response in patients treated for major depression. However, the relationship between genetic variation in deiodinase and T3 treatment response has received little investigation. MethodsThis is a post-hoc analysis of a randomized, double-blind, placebo-controlled trial of concurrent liothyronine (T3-Cytomel®, n = 23; mean dose 46.3 ± 3.3 mcg) in patients with major depression where a clinical recommendation was made to pursue ECT. The primary outcome measure was time to 50% reduction in depressive symptoms. Multivariable linear models were used to examine effect of T3 and placebo and genetic variants as predictors of change in HAMD24 and number of ECT treatments. ResultsSurvival analysis did not show a significant effect for the T3 + ECT group achieving a faster time to response compared to placebo + ECT (p + ECT). Survival analysis for RUL lead placement alone showed a significant effect for the T3 + ECT group achieving a faster time to response compared to p + ECT (p = 0.01) with significantly fewer ECT treatments (p = 0.03). Carriers of the functional SNP rs11206244 gene DI01-C785T minor allele (TT and CT) vs. non-carriers (CC), showed fewer ECT treatments in the T3 + ECT group, compared to p + ECT (5.3 ± 1.0 vs. 8.3 ± 2.1, p = 0.045). ConclusionsThese pilot data identify clinically relevant genetic variation in DI01- C785T contributing to an accelerated response time, but not an overall greater symptom reduction. Exogenous T3 supplementation may be therapeutic by attenuating a baseline DI01 relative functional deficit which functionally reduces peripheral conversion of T4 to biologically active T3. Further work is encouraged to assess genetic variation of thyroid deiodinase enzymes in larger samples of depressed patients to better optimize accelerating strategies to ECT and more broadly, thyroid augmentation strategies in major depressive and bipolar disorders.

Functional Haplotypes and Evolutionary Insight into the Granule-Bound Starch Synthase II (GBSSII) Gene in Korean Rice Accessions (KRICE_CORE).

Granule-bound starch synthase 2 (GBSSII), a paralogous isoform of GBSSI, carries out amylose biosynthesis in rice. Unlike GBSSI, it mainly functions in transient organs, such as leaves. Despite many reports on the starch gene family, little is known about the genetics and genomics of GBSSII. Haplotype analysis was conducted to unveil genetic variations (SNPs and InDels) of GBSSII (OS07G0412100) and it was also performed to gain evolutionary insight through genetic diversity, population genetic structure, and phylogenetic analyses using the KRICE_CORE set (475 rice accessions). Thirty nonsynonymous SNPs (nsSNPs) were detected across the diverse GBSSII coding regions, representing 38 haplotypes, including 13 cultivated, 21 wild, and 4 mixed (a combination of cultivated and wild) varieties. The cultivated haplotypes (C_1–C_13) contained more nsSNPs across the GBSSII genomic region than the wild varieties. Nucleotide diversity analysis highlighted the higher diversity values of the cultivated varieties (weedy = 0.0102, landrace = 0.0093, and bred = 0.0066) than the wild group (0.0045). The cultivated varieties exhibited no reduction in diversity during domestication. Diversity reduction in the japonica and the wild groups was evidenced by the negative Tajima’s D values under purifying selection, suggesting the domestication signatures of GBSSII; however, balancing selection was indicated by positive Tajima’s D values in indica. Principal component analysis and population genetics analyses estimated the ambiguous evolutionary relationships among the cultivated and wild rice groups, indicating highly diverse structural features of the rice accessions within the GBSSII genomic region. FST analysis differentiated most of the classified populations in a range of greater FST values. Our findings provide evolutionary insights into GBSSII and, consequently, a molecular breeding program can be implemented for selecting desired traits using these diverse nonsynonymous (functional) alleles.

Superior japonica rice variety YJ144 with improved rice blast resistance, yield, and quality achieved using molecular design and multiple breeding strategies.

Yanfeng 47 (YF47) is an elite japonica rice variety cultivated in China on nearly 2 million hectares over the past 20 years. However, YF47 is highly susceptible to rice blast (Magnaporthe oryzae), one of the most destructive rice diseases. In this study, we developed novel TPAP (tetra-primer ARMS-PCR) functional markers for the genes Pita, Pib, and Pid2, all of which afford broad-spectrum resistance to blast. A collection of 91 japonica rice germplasms with similar ecological characteristics to YF47 were screened, and Wuyunjing 27 (WYJ27) with Pita and Pib alleles and P135 with the Pid2 allele were identified. Furthermore, the corresponding positive Pita, Pib, and Pid2 alleles were transferred into YF47 using single, mutual, and backcrosses, together with molecular marker-assisted selection (MAS) and anther culture technology. These genetic materials, carrying one, two, or three functional alleles, were generated within 3 years, and compared to YF47, they all showed improved resistance to naturally inoculated rice blast. Further improved lines (IL) 1 to 5 (all containing Pita, Pib, and Pid2 alleles) were evaluated for yield performance, and when no fungicide was applied, all lines except IL-4 showed increased traits compared with those of YF47. IL-5, renamed Yanjing 144 (YJ144), showed yield increases in the Liaoning province regional variety comparison test and superior appearance quality compared to YF47. Our work provides a molecular design strategy for pyramiding multiple beneficial genes to rapidly improve rice blast resistance, yield, and quality using multiple breeding strategies.Supplementary InformationThe online version contains supplementary material available at 10.1007/s11032-021-01259-4.

Registration of ten soft red winter waxy wheat germplasm lines

AbstractWaxy wheat carries null alleles at the three Wx loci encoding the granule‐bound starch synthase I and produces endosperm starch composed of mostly amylopectin with less than 5% amylose. The USDA‐ARS developed and released 10 soft red winter (SRW) waxy wheat germplasm lines, SWQL‐K‐ABD‐1, SWQL‐K‐ABD‐2, SWQL‐K‐ABD‐3, SWQL‐K‐ABD‐4, SWQL‐K‐ABD‐5, SWQL‐W‐ABD‐1, SWQL‐W‐ABD‐2, SWQL‐W‐ABD‐3, SWQL‐W‐ABD‐4, SWQL‐W‐ABD‐5 (Reg. no. GP‐1061 to Reg. no. GP‐1070, PI 698615 to PI 698624), by the introgression of the null alleles at the Wx loci from a soft spring waxy wheat germplasm to two SRW wheat cultivars adapted to the eastern region of the United States. Ten waxy wheat germplasm lines were selected from BC4 or BC5 derivatives of the SRW wheat cultivars ‘Kristy’ and ‘Wilson’ (99ID490/5*Kristy and 99ID490/6*Wilson). The kernel hardness and starch amylose content of 10 SRW waxy wheat germplasm lines ranged from 34.1 to 63.1 and 2.5–7.2%, respectively, while those of wild types and SRW wheat parents carrying the functional alleles at the three Wx loci ranged from 33.9 to 60.4 and 26.8–27.0%, respectively. The starch of the waxy wheat germplasm lines exhibited a lower pasting temperature, higher peak viscosity, and lower setback value than the corresponding wild‐type wheat starch. These waxy wheat germplasm lines would be useful for the development of SRW wheat cultivars carrying different null alleles at the Wx loci that are adapted to the eastern region of the United States.

Identification of limb-specific Lmx1b auto-regulatory modules with Nail-patella syndrome pathogenicity

LMX1B haploinsufficiency causes Nail-patella syndrome (NPS; MIM 161200), characterized by nail dysplasia, absent/hypoplastic patellae, chronic kidney disease, and glaucoma. Accordingly in mice, Lmx1b has been shown to play crucial roles in the development of the limb, kidney and eye. Although one functional allele of Lmx1b appears adequate for development, Lmx1b null mice display ventral-ventral distal limbs with abnormal kidney, eye and cerebellar development, more disruptive, but fully concordant with NPS. In Lmx1b functional knockouts (KOs), Lmx1b transcription in the limb is decreased nearly 6-fold, indicating autoregulation. Herein, we report on two conserved Lmx1b-associated cis-regulatory modules (LARM1 and LARM2) that are bound by Lmx1b, amplify Lmx1b expression with unique spatial modularity in the limb, and are necessary for Lmx1b-mediated limb dorsalization. These enhancers, being conserved across vertebrates (including coelacanth, but not other fish species), and required for normal locomotion, provide a unique opportunity to study the role of dorsalization in the fin to limb transition. We also report on two NPS patient families with normal LMX1B coding sequence, but with loss-of-function variations in the LARM1/2 region, stressing the role of regulatory modules in disease pathogenesis.

Genetic Diversity in Casein Gene Cluster in a Dromedary Camel (C. dromedarius) Population from the United Arab Emirates.

Genetic polymorphisms, causing variation in casein genes (CSN1S1, CSN1S2, CSN2, and CSN3), have been extensively studied in goats and cows, but there are only few studies reported in camels. Therefore, we aimed to identify alleles with functional roles in the United Arab Emirates dromedary camel (Camelus dromedarius) population to complement previous studies conducted on the same species. Using targeted next-generation sequencing, we sequenced all genes in the casein gene cluster in 93 female camels to identify and characterize novel gene variants. Most variants were found in noncoding introns and upstream sequences, but a few variants showed the possibility of functional impact. CSN2 was found to be most polymorphic, with total 91 different variants, followed by CSN1S1, CSN3 and CSN1S2. CSN1S1, CSN1S2 and CSN2 each had at least two variants while CSN3 had only one functional allele. In future research, the functional impact of these variants should be investigated further.

A SmelAAT Acyltransferase Variant Causes a Major Difference in Eggplant (Solanum melongena L.) Peel Anthocyanin Composition.

Eggplant berries are rich in anthocyanins like delphinidin-3-rutinoside (D3R) and nasunin (NAS), which are accumulated at high amounts in the peel. NAS is derived by D3R through acylation and glycosylation steps. The presence of D3R or NAS is usually associated with black-purple or lilac fruit coloration of the most cultivated varieties, respectively. Building on QTL mapping position, a candidate gene approach was used to investigate the involvement of a BAHD anthocyanin acyltransferase (SmelAAT) in determining anthocyanin type. The cDNA sequence comparison revealed the presence of a single-base deletion in D3R-type line ‘305E40’ (305E40_aat) with respect to the NAS-type reference line ‘67/3’. This is predicted to cause a frame shift mutation, leading to a loss of SmelAAT function and, thus, D3R retention. RT-qPCR analyses confirmed SmelAAT and 305E40_aat expression during berry maturation. In D3R-type lines, ‘305E40’ and ‘DR2’, overexpressing the functional SmelAAT allele from ‘67/3’, the transcript levels of the transgene correlated with the accumulation of NAS in fruit peel. Furthermore, it was also found a higher expression of the transcript for glucosyltransferase Smel5GT1, putatively involved with SmelAAT in the last steps of anthocyanin decoration. Finally, an indel marker matching with anthocyanin type in the ‘305E40’ × ’67/3’ segregating population was developed and validated in a wide number of accessions, proving its usefulness for breeding purposes.

Functional homoeologous alleles of CONSTANS contribute to seasonal crop type in rapeseed.

Two CO paralogs in Brassica napus were confirmed and shown distinct expression pattern and function in promoting flowering and allelic variation s within BnaCO.A10 were found closely associated with ecotype divergence. CONSTANS (CO) is a key gene that responds to photoperiod and in Arabidopsis can promote flowering under long-day (LD) conditions. Brassica napus L. is a major oil crop and close relative of Arabidopsis, and arose via allopolyploidization from the diploids B. rapa (A genome) and B. oleracea (C genome). In this study, we confirmed that B. napus has two CO genes located on the A10 (BnaCO.A10) and C9 (BnaCO.C9) chromosomes. Significant differences in level and temporal pattern of transcription, as well as in protein function, of these homoeologous may have resulted from sequence variation in the promoter as well as in the coding region. Apart from two insertions of 527bp and 2002bp in the promoter of BnaCO.C9 that function as transcriptional enhancers, this gene is otherwise highly conserved in both promoter and coding region. However, BnaCO.A10 was classified into two haplotypes and transgene analysis in Arabidopsis and backcross analysis in rapeseed indicated that the winter-type haplotype had a greater effect in promoting flowering than the spring type. We discuss the contribution of CO alleles to species evolution, and for eco-geographic radiation following crop domestication, alongside scope for managing this locus in future breeding.

Confirmation of GmPPR576 as a fertility restorer gene of cytoplasmic male sterility in soybean.

In soybean, heterosis achieved through the three-line system has been gradually applied in breeding to increase yield, but the underlying molecular mechanism remains unknown. We conducted a genetic analysis using the pollen fertility of offspring of the cross NJCMS1A×NJCMS1C. All the pollen of F1 plants was semi-sterile; in F2, the ratio of pollen-fertile plants to pollen-semi-sterile plants was 208:189. This result indicates that NJCMS1A is gametophyte sterile, and the fertility restoration of NJCMS1C to NJCMS1A is a quality trait controlled by a single gene locus. Using bulked segregant analysis, the fertility restorer gene Rf in NJCMS1C was located on chromosome 16 between the markers BARCSOYSSR_16_1067 and BARCSOYSSR_16_1078. Sequence analysis of genes in that region showed that GmPPR576 was non-functional in rf cultivars. GmPPR576 has one functional allele in Rf cultivars but three non-functional alleles in rf cultivars. Phylogenetic analysis showed that the GmPPR576 locus evolved rapidly with the presence of male-sterile cytoplasm. GmPPR576 belongs to the RFL fertility restorer gene family and is targeted to the mitochondria. GmPPR576 was knocked out in soybean N8855 using CRISPR/Cas9. The T1 plants showed sterile pollen, and T2 plants produced few pods at maturity. The results indicate that GmPPR576 is the fertility restorer gene of NJCMS1A.

Inactivation of the germacrene A synthase genes by CRISPR/Cas9 eliminates the biosynthesis of sesquiterpene lactones in Cichorium intybus L.

Chicory (Cichorium intybus var. sativum) is an industrial crop species cultivated for the production of a fructose polymer inulin, which is used as a low‐calorie sweetener and prebiotic. Besides, inulin chicory taproots also accumulate sesquiterpene lactones (STLs). These are bitter tasting compounds, which need to be removed during inulin extraction, resulting in additional costs. In this work, we describe chicory lines where STL accumulation is almost completely eliminated. Genome editing using the CRISPR/Cas9 system was used to inactivate four genes that encode the enzyme that performs the first dedicated step in STL synthesis, germacrene A synthase (CiGAS). Chicory lines were obtained that carried null mutations in all four CiGAS genes. Lines lacking functional CiGAS alleles showed a normal phenotype upon greenhouse cultivation and show nearly complete elimination of the STL synthesis in the roots. It was shown that the reduction in STLs could be attributed to mutations in genetically linked copies of the CiGAS‐short gene and not the CiGAS‐long gene, which is relevant for breeding the trait into other cultivars. The inactivation of the STL biosynthesis pathway led to increase in phenolic compounds as well as accumulation of squalene in the chicory taproot, presumably due to increased availability of farnesyl pyrophosphate (FFP). These results demonstrate that STLs are not essential for chicory growth and that the inhibition of the STL biosynthesis pathway reduced the STL levels chicory which will facilitate inulin extraction.

FOXE1-Dependent Regulation of Macrophage Chemotaxis by Thyroid Cells In Vitro and In Vivo.

Forkhead box E1 (FOXE1) is a lineage-restricted transcription factor involved in thyroid cancer susceptibility. Cancer-associated polymorphisms map in regulatory regions, thus affecting the extent of gene expression. We have recently shown that genetic reduction of FOXE1 dosage modifies multiple thyroid cancer phenotypes. To identify relevant effectors playing roles in thyroid cancer development, here we analyse FOXE1-induced transcriptional alterations in thyroid cells that do not express endogenous FOXE1. Expression of FOXE1 elicits cell migration, while transcriptome analysis reveals that several immune cells-related categories are highly enriched in differentially expressed genes, including several upregulated chemokines involved in macrophage recruitment. Accordingly, FOXE1-expressing cells induce chemotaxis of co-cultured monocytes. We then asked if FOXE1 was able to regulate macrophage infiltration in thyroid cancers in vivo by using a mouse model of cancer, either wild type or with only one functional FOXE1 allele. Expression of the same set of chemokines directly correlates with FOXE1 dosage, and pro-tumourigenic M2 macrophage infiltration is decreased in tumours with reduced FOXE1. These data establish a novel link between FOXE1 and macrophages recruitment in the thyroid cancer microenvironment, highlighting an unsuspected function of this gene in the crosstalk between neoplastic and immune cells that shape tumour development and progression.

Interplay of the RNA Exosome Complex and RNA-Binding Protein Ssd1 in Maintaining Cell Wall Stability in Yeast.

ABSTRACTYeast cell wall stability is important for cell division and survival under stress conditions. The expression of cell-wall-related proteins is regulated by several pathways involving RNA-binding proteins and RNases. The multiprotein RNA exosome complex provides the 3′→5′ exoribonuclease activity that is critical for maintaining the stability and integrity of the yeast cell wall under stress conditions such as high temperatures. In this work, we show that the temperature sensitivity of RNA exosome mutants is most pronounced in the W303 genetic background due to the nonfunctional ssd1-d allele. This gene encodes the RNA-binding protein Ssd1, which is involved in the posttranscriptional regulation of cell-wall-related genes. Expression of the functional SSD1-V allele from its native genomic locus or from a centromeric plasmid suppresses the growth defects and aberrant morphology of RNA exosome mutant cells at high temperatures or upon treatment with cell wall stressors. Moreover, combined inactivation of the RNA exosome catalytic subunit Rrp6 and Ssd1 results in a synthetically sick phenotype of cell wall instability, as these proteins may function in parallel pathways (i.e., via different mRNA targets) to maintain cell wall stability.IMPORTANCE Stressful conditions such as high temperatures can compromise cellular integrity and cause bursting. In microorganisms surrounded by a cell wall, such as yeast, the cell wall is the primary shield that protects cells from environmental stress. Therefore, remodeling its structure requires inputs from multiple signaling pathways and regulators. In this work, we identify the interplay of the RNA exosome complex and the RNA-binding protein Ssd1 as an important factor in the yeast cell wall stress response. These proteins operate in independent pathways to support yeast cell wall stability. This work highlights the contribution of RNA-binding proteins in the regulation of yeast cell wall structure, providing new insights into yeast physiology.

The timing of genetic degeneration of sex chromosomes.

Genetic degeneration is an extraordinary feature of sex chromosomes, with the loss of functions of Y-linked genes in species with XY systems, and W-linked genes in ZW systems, eventually affecting almost all genes. Although degeneration is familiar to most biologists, important aspects are not yet well understood, including how quickly a Y or W chromosome can become completely degenerated. I review the current understanding of the time-course of degeneration. Degeneration starts after crossing over between the sex chromosome pair stops, and theoretical models predict an initially fast degeneration rate and a later much slower one. It has become possible to estimate the two quantities that the models suggest are the most important in determining degeneration rates-the size of the sex-linked region, and the time when recombination became suppressed (which can be estimated using Y-X or W-Z sequence divergence). However, quantifying degeneration is still difficult. I review evidence on gene losses (based on coverage analysis) or loss of function (by classifying coding sequences into functional alleles and pseudogenes). I also review evidence about whether small genome regions degenerate, or only large ones, whether selective constraints on the genes in a sex-linked region also strongly affect degeneration rates, and about how long it takes before all (or almost all) genes are lost. This article is part of the theme issue 'Challenging the paradigm in sex chromosome evolution: empirical and theoretical insights with a focus on vertebrates (Part I)'.

Combinations of Ghd7, Ghd8, and Hd1 determine strong heterosis of commercial rice hybrids in diverse ecological regions.

Heterosis of grain yield is closely associated with heading date in crops. Gene combinations of the major heading date genes Ghd7, Ghd8, and Hd1 play important roles in enhancing grain yield and adaptation to ecological regions in rice. However, the predominant three-gene combinations for a specific ecological region remain unclear in both three-line and two-line hybrids. In this study, we sequenced these three genes of 50 cytoplasmic male sterile/maintainer lines, 31 photo-thermo-sensitive genic male sterile lines, and 109 restorer lines. Sequence analysis showed that hybrids carrying strong functional alleles of Ghd7 and Hd1 and non-functional Ghd8 are predominant in three-line hybrids and are recommended for rice production in the subtropics around 30°N/S. Hybrids carrying strong functional Ghd7 and Ghd8 and non-functional Hd1 are predominant in two-line hybrids and are recommended for low latitude areas around 23.5°N/S rich in photothermal resources. Hybrids carrying strong functional Ghd7 and Ghd8 and functional Hd1 were not identified in commercial hybrids in the middle and lower reaches of the Yangtze River, but they have high yield potential in tropical regions because they have the strongest photoperiod sensitivity. Based on these findings, two genic sterile lines, Xiangling 628S and C815S, whose hybrids often head very late, were diagnosed with these three genes, and Hd1 was targeted to be knocked out in Xiangling 628S and replaced with hd1 in C815S. The hybrids developed from both modified sterile lines in turn had appropriate heading dates and significantly improved grain yield. This study provides new insights for breeding design to develop hybrids for various regions.

Genetic diversity in wild species and cultivars of strawberry for the FanAAMT gene controlling fruit flavor volatiles

Background. An important consumer trait of strawberry fruits is their aroma. Methyl anthranilate makes a considerable contribution to the fruit flavor. The methyl anthranilate content in strawberry fruits is controlled by the FanAAMT (аnthranilic acid methyltransferase) gene. Identification of genetic determinants for this trait facilitates targeted selection of promising forms based on diagnostic DNA markers. The purpose of this study was to study the allelic diversity of the FanAAMT fruit flavor gene in wild strawberry species and strawberry cultivars for identification of promising genotypes.Materials and methods. The objects of this study were wild species of Fragaria L. as well as F. × anaschata Kantor. and F. × ananassa Duch. cultivars of different ecogeographic origin. The FanAAMT gene was identified with the dominant marker FanAAMT.Results and conclusion. In the analyzed collection of strawberry genotypes, the FanAAMT gene was identified in 36.4% of the forms, including the wild species F. vesca L., F. moschata Duch. and F. virginiana subsp. platypetala (Rydb.) Staudt, and cv. ‘Kupchikha’ (F. × anaschata). Among the analyzed F. × ananassa cultivars, the FanAAMT gene was found in 31.6% of the tested forms, specifically in 27.3% of the 22 Russian cultivars, and 37.5% of the analyzed foreign ones. Promising sources of high methyl anthranilate content in fruits were identified: wild spp. F. moschata, F. vesca, and F. virginiana subsp. platypetala; cv. ‘Kupchikha’ (F. × anaschata); Russian garden strawberry cvs. ‘Bylinnaya’, ‘Zenit’, ‘Lastochka’, ‘Neznakomka’, ‘Feyerverk’ and ‘Tsarskoselskaya’; and foreign garden strawberry cvs. ‘Karmen’, ‘Ostara’, ‘Samson’, ‘Symphony’, ‘Troubadour’ and ‘Vima Tarda’, in which the functional allele of the FanAAMT gene was found. In the remaining studied strawberry genotypes the marker FanAAMT was not detected, which presumably indicates that the FanAAMT gene is absent. cells (R9.4.1).

Mapping of a Major QTL, <i>qHD6-SD</i> Responsible for Days to heading Under Natural Short Day Conditions to Develop Rice Varieties adaptable to Tropical Regions

In the tropics (Southeast Asian countries), indica rice is more common than japonica. Japonica rice is mainly cultivated in temperate regions, including Korea, Japan, and China (northeast regions) due to its poor adaptation to tropical areas. To develop tropically-adapted high-yielding japonica rice, breeders should overcome the challenges, including extremely early flowering, low biomass accumulation, and inferior panicle traits. This study investigated 180 F9 recombinant inbred lines (RILs) developed from a cross between Ilpum (temperate japonica) and Zenith (indica) as a case population to identify quantitative trait loci (QTLs) that influence the said traits. Here we identified two major QTLs, qHD6-SD and qHD6- LD, conferring days to heading under short day (SD) and long day (LD) conditions, respectively. Finer mapping revealed that both qHD6-SD and qHD6-LD located in the similar 98 kb region harbored the Hd1 gene. Days to heading in the RILs harboring the Zenith allele type of qHD6-SD under SD conditions were significantly longer than those in the RILs harboring the Ilpum allele type. On the contrary, days to heading in the RILs harboring the Zenith allele type of qHD6-SD under LD conditions were significantly shorter than those in the RILs harboring the Ilpum allele type. This bi-functionality of qHD6-SD upon heading strongly support the claim that both qHD6-SD and qHD6-LD might be the Hd1 gene. Our findings further support the claim that the functional allele type of Hd1 gene delays long-day heading and promotes extremely early short-day heading. Therefore, a non-functional Hd1 type is critical to tropical adaptation of japonica rice since it delays the heading date, which is essential to attain prolonged vegetative state in order to achieve optimum biomass, increased spikelet number, and grain filling capacity.

LEAFY COTYLEDON1 expression in the endosperm enables embryo maturation in Arabidopsis

The endosperm provides nutrients and growth regulators to the embryo during seed development. LEAFY COTYLEDON1 (LEC1) has long been known to be essential for embryo maturation. LEC1 is expressed in both the embryo and the endosperm; however, the functional relevance of the endosperm-expressed LEC1 for seed development is unclear. Here, we provide genetic and transgenic evidence demonstrating that endosperm-expressed LEC1 is necessary and sufficient for embryo maturation. We show that endosperm-synthesized LEC1 is capable of orchestrating full seed maturation in the absence of embryo-expressed LEC1. Inversely, without LEC1 expression in the endosperm, embryo development arrests even in the presence of functional LEC1 alleles in the embryo. We further reveal that LEC1 expression in the endosperm begins at the zygote stage and the LEC1 protein is then trafficked to the embryo to activate processes of seed maturation. Our findings thus establish a key role for endosperm in regulating embryo development.

NANOS2 is a sequence-specific mRNA-binding protein that promotes transcript degradation in spermatogonial stem cells

SummarySpermatogonial stem cells (SSCs) sustain spermatogenesis and fertility throughout adult male life. The conserved RNA-binding protein NANOS2 is essential for the maintenance of SSCs, but its targets and mechanisms of function are not fully understood. Here, we generated a fully functional epitope-tagged Nanos2 mouse allele and applied the highly stringent cross-linking and analysis of cDNAs to define NANOS2 RNA occupancy in SSC lines. NANOS2 recognizes the AUKAAWU consensus motif, mostly found in the 3′ untranslated region of defined messenger RNAs (mRNAs). We find that NANOS2 is a regulator of key signaling and metabolic pathways whose dosage or activity are known to be critical for SSC maintenance. NANOS2 interacts with components of CCR4-NOT deadenylase complex in SSC lines, and consequently, NANOS2 binding reduces the half-lives of target transcripts. In summary, NANOS2 contributes to SSC maintenance through the regulation of target mRNA stability and key self-renewal pathways.

Elite sd1 alleles in japonica rice and their breeding applications in northeast China

The Green Revolution gene sd1 has been used extensively in modern rice breeding, especially in indica cultivars. However, elite sd1 alleles and related germplasm resources used for japonica rice breeding have not been identified, and extensive efforts are needed for japonica rice breeding to obtain new dwarfing sources. Data from MBKbase-Rice revealed seven sd1 haplotypes in indica and four in japonica rice. Two new sd1 alleles were identified in indica rice. In 295 japonica accessions from northeast Asia, except for the weak functional allele SD1-EQ, sd1-r was the major allele, reducing plant height in comparison with SD1-EQ. Japonica germplasm resources carrying reported sd1 alleles were identified by genotype searching and further verified by literature search, genealogical analysis, and dCaps markers. Pedigrees and geographic distribution showed that sd1-r is an excellent allele widely used in northern China and Tohoku in Japan, and sd1-j is commonly used in east China and Kyushu in Japan. Dongnong- and Xiushui-series cultivars carrying sd1-r and sd1-j, respectively, are essential branches of the backbone parents of Chinese japonica rice, Akihikari and Ce21, with the largest number of descendants and derived generations. In semi-dwarf japonica rice breeding, sd1-d was introgressed into Daohuaxiang 2 (DHX2). Dwarf and semi-dwarf lines carrying sd1-d were selected and designated as 1279 and 1280, respectively, after withstanding typhoon-induced strong winds and heavy rains in 2020, and are anticipated to become useful intermediate materials for future genetic research and breeding. This work will facilitate the introduction, parental selection, and marker-assisted breeding, and provide a material basis for the next step in identifying favorable genes that selected together with the sd1 alleles in japonica backbone parents.

A Multitubular Kidney-on-Chip to Decipher Pathophysiological Mechanisms in Renal Cystic Diseases.

Autosomal Dominant Polycystic Kidney Disease (ADPKD) is a major renal pathology provoked by the deletion of PKD1 or PKD2 genes leading to local renal tubule dilation followed by the formation of numerous cysts, ending up with renal failure in adulthood. In vivo, renal tubules are tightly packed, so that dilating tubules and expanding cysts may have mechanical influence on adjacent tubules. To decipher the role of this coupling between adjacent tubules, we developed a kidney-on-chip reproducing parallel networks of tightly packed tubes. This original microdevice is composed of cylindrical hollow tubes of physiological dimensions, parallel and closely packed with 100–200 μm spacing, embedded in a collagen I matrix. These multitubular systems were properly colonized by different types of renal cells with long-term survival, up to 2 months. While no significant tube dilation over time was observed with Madin-Darby Canine Kidney (MDCK) cells, wild-type mouse proximal tubule (PCT) cells, or with PCT Pkd1+/- cells (with only one functional Pkd1 allele), we observed a typical 1.5-fold increase in tube diameter with isogenic PCT Pkd1-/- cells, an ADPKD cellular model. This tube dilation was associated with an increased cell proliferation, as well as a decrease in F-actin stress fibers density along the tube axis. With this kidney-on-chip model, we also observed that for larger tube spacing, PCT Pkd1-/- tube deformations were not spatially correlated with adjacent tubes whereas for shorter spacing, tube deformations were increased between adjacent tubes. Our device reveals the interplay between tightly packed renal tubes, constituting a pioneering tool well-adapted to further study kidney pathophysiology.