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Key message: We developed an efficient promoter editing method to create different weak Ehd1 alleles in elite japonica rice variety ZJ8 with slightly delayed heading and improved yield for use in breeding. Heading date is an important agronomic trait of rice (Oryza sativa) that determines the planting areas and cultivation seasons of different varieties, thus affecting final yield. Early heading date 1 (Ehd1) is a major rice integrator gene in the regulatory network of heading date whose expression level is negatively correlated with heading date and grain yield. Some elite japonica varieties such as Zhongjia 8 (ZJ8) show very early heading with poor agronomic traits when planted in South China. This problem can be addressed by downregulating the expression of Ehd1. In this study, we analyzed the cis-regulatory elements in the Ehd1 promoter region. We then used CRISPR/Cas9-mediated editing to modify the Ehd1 promoter at multiple target sites in ZJ8. We rapidly identified homozygous allelic mutations in the T2 generation via long-read sequencing. We obtained several Ehd1 promoter mutants with different degrees of lower Ehd1 expression, delayed heading date, and improved yield-related traits. We developed an efficient promoter editing method to create different weak Ehd1 alleles for breeding selection. Using this method, a series of heading date materials from elite varieties can be created to expand the planting area of rice and improve grain yields. [ABSTRACT FROM AUTHOR]

Key message: We clarify the influence of the genotypes of the heading date genes Hd1, Ghd7, DTH8, and PRR37 and their combinations on yield-related traits and the functional differences between different haplotypes. Heading date is a key agronomic trait in rice (Oryza sativa L.) that determines yield and adaptability to different latitudes. Heading date 1 (Hd1), Grain number, plant height, and heading date 7 (Ghd7), Days to heading on chromosome 8 (DTH8), and PSEUDO-RESPONSE REGULATOR 37 (PRR37) are core rice genes controlling photoperiod sensitivity, and these genes have many haplotypes in rice cultivars. However, the effects of different haplotypes at these genes on yield-related traits in diverse rice materials remain poorly characterized. In this study, we knocked out Hd1, Ghd7, DTH8, or PRR37, alone or together, in indica and japonica varieties and systematically investigated the agronomic traits of each knockout line. Ghd7 and PRR37 increased the number of spikelets and improved yield, and this effect was enhanced with the Ghd7 DTH8 or Ghd7 PRR37 combination, but Hd1 negatively affected yield. We also identified a new weak functional Ghd7 allele containing a mutation that interferes with splicing. Furthermore, we determined that the promotion or inhibition of heading date by different PRR37 haplotypes is related to PRR37 expression levels, day length, and the genetic background. For rice breeding, a combination of functional alleles of Ghd7 and DTH8 or Ghd7 and PRR37 in the hd1 background can be used to increase yield. Our study clarifies the effects of heading date genes on yield-related traits and the functional differences among their different haplotypes, providing valuable information to identify and exploit elite haplotypes for heading date genes to breed high-yielding rice varieties. [ABSTRACT FROM AUTHOR]

Concrete grinding residue (CGR) is a byproduct of diamond grinding, a road surface maintenance technique. Direct deposition of CGR along roadsides may influence plant growth, which has not been fully studied. Particularly, systematic experiments of CGR effects on selected common prairie species growth under controlled environments are rarely reported. Thus, in this study, a greenhouse experiment was performed to determine CGR effects on seedling emergence and aboveground biomass for four roadside prairie species: Indian grass, Canada wild rye, partridge pea, and wild bergamot. Nicollet loam and Hanlon fine sandy loam were used, and CGR of 4 rates, 0, 2.24, 4.48, and 8.96 kg m−2, were applied in two ways, either mixed with the soil or applied on the soil surface. Multiple comparisons indicate that CGR produced mixed impacts on seedling emergence, depending on plant species, while aboveground biomass is not significantly influenced by CGR in general. ANOVA analysis with stepwise linear regression indicates that CGR had no uniform effects on seedling emergence, and CGR impacts should be studied for specific plant species and soil types. In conclusion, while CGR may lead to negative environmental issues on roadside plants depending on the plant species and soil types, if aboveground biomass is a major consideration, CGR effects are negligible. This study provides reference information for regulating CGR depositions along roadsides. Future studies may focus on investigating the relationship between CGR effects on seedling emergence and species succession in actual roadside environments. [ABSTRACT FROM AUTHOR]

Aims: Populus can tolerant high concentration Al stress. However, the mechanisms of Mg alleviation to Al toxicity in populus remain unknown. Methods: In the present study, adequate Mg was supplied to poplar under high concentration Al toxicity stress, and the pH gradients of root surface, Mg and Al uptake from root apex were detected using electrophysiological analysis, fluorescence staining, etc. Furthermore, auxin distribution and transport dynamic kinetics in root tips were also detected. Results: In the present study, we found that adequate supply of Mg alleviated high concentration Al toxicity to populus root growth. Mg promoted the pH gradients of root surface in populus, leading to alkalization in the root transition zone, which prevented Al toxicity to root elongation. The auxin distribution in root tips of populus was detected using DR5:GFP reporter. The transport and distribution of polar auxin in root transition zone were inhibited by Al toxicity, but partially alleviated by Mg supply. Further electrophysiological experiments using auxin transporter mutant pin-formed 2 (pin2) showed that Mg alleviated Al toxicity by PIN2-based polar auxin transport, which regulated root surface alkalization in the transition zone. Transcriptomic analysis and yeast complementation experiments using mrs2 mutants also reveals same relationships among Mg, auxin and Al. Conclusions: The present study suggests that Mg promotes polar auxin transport and distribution, which leads to the elevated root surface pH regulation, and further alleviates the Al toxicity. Our results partially clarify the mechanism of Mg in alleviating the toxicity of high concentration Al in woody plants. [ABSTRACT FROM AUTHOR]

Background and aims: Magnesium (Mg) deficiency impacts many metabolic processes in Brassica napus (B. napus), leading to yield loss. However, the mechanism of Mg2+ uptake and translocation in B. napus remains unknown. Methods: After screening 39 genotypes of B. napus under Mg-deficient conditions, the cultivars P160 and P153 were selected according to their Mg transfer factor (TF) from root to shoot. We further characterized these two genotypes under Mg-deficiency by analyzing chlorophyll concentration, malondialdehyde and peroxidase activity, and reducing sugar concentration in leaves. Additionally, we performed transcriptomics and qRT-PCR assays on P153 and P160 shoots and roots. The identified functional genes involved in Mg transport were characterized by functional assays in yeast and Arabidopsis mutants. Results: The physiological analysis revealed that P160 (Mg tolerance cultivar; Mg-T) is more tolerant than P153 (Mg sensitive cultivar; Mg-S) under magnesium-deficient environments. Transcriptomics and qRT-PCR assays revealed that transcript levels of BnMGT1–2 and BnMGT6–1 were more significantly up-regulated in the shoot of Mg-T cultivar than that of the Mg-S cultivar under Mg limitation. Functional assays of BnMGT1–2 and BnMGT6–1 reveals that BnMGT1–2 and BnMGT6–1 are the two main functional Mg transporters mediating Mg translocation from root to shoot under low Mg conditions. Conclusion: Mg-T is more efficient in the translocation of Mg from root to shoot than Mg-S. BnMGT1–2 and BnMGT6–1 should be the two main Mg transporters associated with Mg translocation under Mg deficiency condition, which caused the different Mg efficiency between the Mg-T and Mg-S. [ABSTRACT FROM AUTHOR]

Aims: Cadmium (Cd) is the most widespread toxic heavy metal to plant growth. As the second leading oil crop, some genotypes of Brassica napus (B. napus) are potential Cd accumulators. However, the Cd translocation mechanism from root to shoot in B. napus in response to Cd toxicity remains unknown. Methods: In the present study, a couple of B. napus genotypes with contrasting Cd uptake and root-to-shoot translocation abilities, named P78 (the high Cd accumulator, HC) and P72 (the low Cd accumulator, LC), were chosen from 39 B. napus genotypes with various Cd accumulation features. Results: Physiological comparison of P78 and P72 reveals that P72 is more sensitive to Cd toxicity than P78. With genomic resequencing, transcriptomics and qRT-PCR assay, BnNramp2;1 and BnNramp4;2 were focused with highly upregulation in shoot of P78 under Cd treatment condition. Furthermore, BnNramp2;1 and BnNramp4;2 can successfully complement the function of tonoplast localized Cd transporter YCF1. And when BnNramp2;1 and BnNramp4;2 were transferred in Arabidopsis atnramp mutants, the transgenic plants showed better growth rate than mutants under higher Cd stress conditions. Conclusions: The results reveals that BnNramp2;1 and BnNramp4;2 were two main Cd transporters associated with enhanced root-to-shoot translocation and accumulation of Cd in shoot of B. napus. [ABSTRACT FROM AUTHOR]

The study of Mendelian diseases and the identification of their causative genes are of great significance in the field of genetics. The evaluation of the pathogenicity of genes and the total number of Mendelian disease genes are both important questions worth studying. However, very few studies have addressed these issues to date, so we attempt to answer them in this study. We calculated the gene pathogenicity prediction (GPP) score by a machine learning approach (random forest algorithm) to evaluate the pathogenicity of genes. When we applied the GPP score to the testing gene set, we obtained an accuracy of 80%, recall of 93% and area under the curve of 0.87. Our results estimated that a total of 10,384 protein-coding genes were Mendelian disease genes. Furthermore, we found the GPP score was positively correlated with the severity of disease. Our results indicate that GPP score may provide a robust and reliable guideline to predict the pathogenicity of protein-coding genes. To our knowledge, this is the first trial to estimate the total number of Mendelian disease genes. [ABSTRACT FROM AUTHOR]

In this paper, we mine full mtDNA sequences from an exome capture data set of 2000 Danes, showing that it is possible to get high-quality full-genome sequences of the mitochondrion from this resource. The sample includes 1000 individuals with type 2 diabetes and 1000 controls. We characterise the variation found in the mtDNA sequence in Danes and relate the variation to diabetes risk as well as to several blood phenotypes of the controls but find no significant associations. We report 2025 polymorphisms, of which 393 have not been reported previously. These 393 mutations are both very rare and estimated to be caused by very recent mutations but individuals with type 2 diabetes do not possess more of these variants. Population genetics analysis using Bayesian skyline plot shows a recent history of rapid population growth in the Danish population in accordance with the fact that >40% of variable sites are observed as singletons. [ABSTRACT FROM AUTHOR]

For 10,000?years pigs and humans have shared a close and complex relationship. From domestication to modern breeding practices, humans have shaped the genomes of domestic pigs. Here we present the assembly and analysis of the genome sequence of a female domestic Duroc pig (Sus scrofa) and a comparison with the genomes of wild and domestic pigs from Europe and Asia. Wild pigs emerged in South East Asia and subsequently spread across Eurasia. Our results reveal a deep phylogenetic split between European and Asian wild boars ?1 million years ago, and a selective sweep analysis indicates selection on genes involved in RNA processing and regulation. Genes associated with immune response and olfaction exhibit fast evolution. Pigs have the largest repertoire of functional olfactory receptor genes, reflecting the importance of smell in this scavenging animal. The pig genome sequence provides an important resource for further improvements of this important livestock species, and our identification of many putative disease-causing variants extends the potential of the pig as a biomedical model. [ABSTRACT FROM AUTHOR]

Germline inactivating mutations of the breast cancer associated gene 1 (BRCA1) predispose to breast cancer and account for most cases of familiar breast and/or ovarian cancer. The pig is an excellent model for medical research as well as testing of new methods and drugs for disease prevention and treatment. We have generated cloned BRCA1 knockout (KO) Yucatan miniature piglets by targeting exon 11 using recombinant adeno-associated virus (rAAV)-mediated gene targeting and somatic cell nuclear transfer by Handmade Cloning (HMC). We found a very high targeting rate of rAAV-mediated BRCA1 KO. Approximately 35% of the selected cells were BRCA1 targeted. One BRCA1 KO cell clone (5D1), identified by PCR and Southern blot, was used as nuclear donor for HMC. Reconstructed embryos were transferred to three recipient sows which gave birth to 8 piglets in total. Genotyping identified seven piglets as BRCA1 heterozygotes (BRCA1), and one as wild type. The BRCA1 expression was decreased at the mRNA level in BRCA1 fibroblasts. However, all BRCA1 piglets died within 18 days after birth. The causes of perinatal mortality remain unclear. Possible explanations may include a combination of the BRCA1 haploinsufficiency, problems of epigenetic reprogramming, presence of the marker gene, single cell clone effects, and/or the special genetic background of the minipigs. [ABSTRACT FROM AUTHOR]

We describe a genetic variation map for the chicken genome containing 2.8 million single-nucleotide polymorphisms (SNPs). This map is based on a comparison of the sequences of three domestic chicken breeds (a broiler, a layer and a Chinese silkie) with that of their wild ancestor, red jungle fowl. Subsequent experiments indicate that at least 90% of the variant sites are true SNPs, and at least 70% are common SNPs that segregate in many domestic breeds. Mean nucleotide diversity is about five SNPs per kilobase for almost every possible comparison between red jungle fowl and domestic lines, between two different domestic lines, and within domestic lines-in contrast to the notion that domestic animals are highly inbred relative to their wild ancestors. In fact, most of the SNPs originated before domestication, and there is little evidence of selective sweeps for adaptive alleles on length scales greater than 100?kilobases. [ABSTRACT FROM AUTHOR]

To find unknown protein-coding genes, annotation pipelines use a combination of ab initio gene prediction and similarity to experimentally confirmed genes or proteins. Here, we show that although the ab initio predictions have an intrinsically high false-positive rate, they also have a consistently low false-negative rate. The incorporation of similarity information is meant to reduce the false-positive rate, but in doing so it increases the false-negative rate. The crucial variable is gene size (including introns) - genes of the most extreme sizes, especially very large genes, are most likely to be incorrectly predicted. [ABSTRACT FROM AUTHOR]

We compared technetium-99m methoxyisobutylisonitrile (MIBI) myocardial perfusion single-photon emission tomography (SPET) (MPS) and electron beam computed tomography (EBCT) in order to assess their respective value in the detection of coronary artery disease (CAD). [sup 99m]Tc-MIBI SPET (stress-resting) and EBCT studies were performed in 51 patients with suspected CAD who underwent coronary angiography (CAG). CAG showed that of the 51 patients, 36 had coronary stenosis ≥50% while 15 had normal results. A moderate positive rank correlation was found between coronary calcification detected by EBCT and MPS score (r[sub s]=0.5283, P<0.01). The concordance between EBCT and MPS for the evaluation of CAD was 72.5% (37/51). The sensitivity of EBCT in detecting CAD in 51 patients was comparable to that of MPS (81% vs 94%, NS). However, the accuracy of EBCT was lower than that of MPS (78% vs 94%, P<0.025). As regards the detection of individual coronary artery disease, there was no significant difference in sensitivity between EBCT and MPS (65% vs 75%, NS); however, the specificity and accuracy of EBCT were lower than those of MPS (specificity: 77% vs 95%, P<0.005; accuracy 71% vs 85%, P<0.005). The sensitivity, specificity and accuracy of MPS in detecting single-vessel disease were higher than those of EBCT (sensitivity: 86% vs 42%, P<0.025; specificity: 96% vs 70%, P<0.025; accuracy: 93% vs 61%, P<0.005). However, no significant differences in the sensitivity, specificity and accuracy of MPS and EBCT were found in respect of multivessel disease. In conclusion: [sup 99m]Tc-MIBI myocardial perfusion SPET and EBCT provide different information in the assessment of CAD. The sensitivity of EBCT for the detection of CAD is comparable with that of MPS; however, the specificity and accuracy of EBCT are lower than those of MPS. More reliable results will be obtained if both myocardial perfusion SPET and EBCT are performed. [ABSTRACT FROM AUTHOR]