Previous studies have revealed the miR164 family and the miR164-targeted NAC transcription factor genes in rice (Oryza sativa) and Arabidopsis that play versatile roles in developmental processes and stress responses.  In wheat (Triticum aestivum L.), we found nine genetic loci of tae-miR164 (tae-MIR164 a to i) producing two mature sequences that down-regulate the expression of three newly identified target genes of TaNACs (TaNAC1, TaNAC11, and TaNAC14) by the cleavage of the respective mRNAs.  Overexpression of tae-miR164 or one of its target genes (TaNAC14) demonstrated that the miR164-TaNAC14 module greatly affects root growth and development and stress (drought and salinity) tolerance in wheat seedlings, and TaNAC14 promotes root growth and development in wheat seedlings and enhances drought tolerance, while tae-miR164 inhibits root development and reduces drought and salinity tolerance by down-regulating the expression of TaNAC14.  These findings identify the miR164-TaNAC14 module as well as other tae-miR164-regulated genes which can serve as new genetic resources for stress-resistance wheat breeding.

Plant chlorophyll biosynthesis and chloroplast development are two complex processes that are regulated by exogenous and endogenous factors.  In this study, we identified OsDXR, a gene encoding a reductoisomerase that positively regulates chlorophyll biosynthesis and chloroplast development in rice.  OsDXR knock-out lines displayed the albino phenotype and could not complete the whole life cycle process.  OsDXR was highly expressed in rice leaves, and subcellular localization indicated that OsDXR is a chloroplast protein.  Many genes involved in chlorophyll biosynthesis and chloroplast development were differentially expressed in the OsDXR knock-out lines compared to the wild type.  Moreover, we found that the RNA editing efficiencies of ndhA-1019 and rpl2-1 were significantly reduced in the OsDXR knock-out lines.  Furthermore, OsDXR interacted with the RNA editing factor OsMORF1 in a yeast two-hybrid screen and bimolecular fluorescence complementation assay.  Finally, disruption of the plastidial 2-C-methyl-derythritol-4-phosphate pathway resulted in defects in chloroplast development and the RNA editing of chloroplast genes.

Omega-3 (linolenic acid (ALA), docosapentaenoic acid, eicosapentaenoic acid) and omega-6 (linoleic acid (LA), arachidonic acid) polyunsaturated fatty acids are essential for health and normal physiological functioning in humans.  Here we report a genome-wide association study (GWAS) on LA content in chicken meat.  The 19 significant single nucleotide polymorphisms (SNPs) identified by the GWAS approach were annotated in VILL, PLCD1 and OXSR1 genes with highly polymorphic linkage blocks, and explained 4.5% of the phenotypic variation in the LA content.  Specifically, the PLCD1 mRNA expression level was negatively correlated with the LA content, and significantly higher in chickens with low LA content than in those with high LA content.  In addition, PLCD1 was found to be involved in metabolic pathways, etc.  Furthermore, the LA content was correlated with volatile organic compounds (e.g., octanal, etc.), but no relationship was found with intramuscular fat and triglycerides in chicken meat.  The results indicated that there are key SNPs in PLCD1 that regulate the content of LA, and it has no significant effect on fat deposition, but may affect the content of volatile organic compounds (VOCs).

Understanding the heterosis in multiple environments between different heterotic groups is of fundamental importance in successful maize breeding.  A total of 737 hybrids derived from 41 maize inbreds were evaluated over two years, with the aim of assessing the genetic diversity and their performance between heterotic groups under drought-stressed (DS) and well-watered (WW) treatments.  A total of 38 737 SNPs were employed to assess the genetic diversity.  The genetic distance (GD) between the parents ranged from 0.05 to 0.74, and the 41 inbreds were classified into five heterotic groups.  According to the hybrid performance (high yield and early maturity between heterotic groups), the heterosis and heterotic patterns of Iowa Stiff Stalk Synthetic (BSSS)×Non-Stiff Stalk (NSS), NSS×Sipingtou (SPT) and BSSS×SPT were identified to be useful options in China’s maize breeding.  The relative importance of general and specific combining abilities (GCA and SCA) suggests the importance of the additive genetic effects for grain yield traits under the WW treatment, but the non-additive effects under the DS treatment.  At least one of the parental lines with drought tolerance and a high GCA effect would be required to achieve the ideal hybrid performance under drought conditions.  GD showed a positive correlation with yield and yield heterosis in within-group hybrids over a certain range of GD.  The present investigation suggests that the heterosis is due to the combined accumulation of superior genes/alleles in parents and the optimal genetic distance between parents, and that yield heterosis under DS treatment was mainly determined by the non-additive effects.

Improving the production of broiler chicken meat has been a goal of broiler breeding programs worldwide for many years.  However, the genetic architectures of skeletal muscle production traits in chickens have not yet been fully elucidated.  In the present study, a total of 519 F₂ birds, derived from a cross of Arbor Acres broiler and Baier layer, were re-sequenced (26 F₀ individuals were re-sequenced at a 10-fold depth; 519 F₂ individuals were re-sequenced at a 3-fold depth) and the coupling of genome-wide association study (GWAS) and selection signatures (F_ST (fixation index) and θ_π (nucleotide diversity)) was carried out to pinpoint the associated loci and genes that contribute to pectoral muscle weight (PMW) and thigh muscle weight (TMW).  A total of 7 890 258 single nucleotide polymorphisms (SNPs) remained to be analyzed after quality control and imputation.  The integration of GWAS and selection signature analyses revealed that genetic determinants responsible for skeletal muscle production traits were mainly localized on chromosomes 1 (168.95–172.43 Mb) and 4 (74.37–75.23 Mb).  A total of 17 positional candidate genes (PCGs) (LRCH1, CDADC1, CAB39L, LOC112531568, LOC112531569, FAM124A, FOXO1, NBEA, GPALPP1, RUBCNL, ARL11, KPNA3, LHFP, GBA3, LOC112532426, KCNIP4, and SLIT2) were identified in these regions.  In particular, KPNA3 and FOXO1 were the most promising candidates for meat production in chickens.  These findings will help enhance our understanding of the genetic architecture of chicken muscle production traits, and the significant SNPs identified could be promising candidates for integration into practical breeding programs such as genome-wide selection (GS) to improve the meat yield of chickens.

Indigenous chicken products are increasingly favored by consumers due to their unique meat and egg quality.  However, the relatively poor egg-laying performance largely impacts the economic benefits and hinders sustainable development of the local chicken industry.  Thus, excavating key genes and effective molecular markers associated with egg-laying performance is necessary to improve egg production via genetic selection in indigenous breeds.  In the present study, comparative hypothalamic transcriptome between pre-laying (15 weeks old) and peak-laying (30 weeks old) Lushi blue-shelled-egg (LBS) chicken was performed.  A total of 518 differentially expressed genes (DEGs) were identified.  Among the DEGs, 64 genes were enriched in 10 Gene Ontology (GO) terms associated with reproductive regulation via GO analysis and considered as potential candidate genes regulating egg-laying performance.  Of the 64 genes, 16 showed high connectivity (degree≥12) by protein–protein interaction (PPI) network analysis and were considered as potential core candidate genes (PCCGs).  To further look for key candidate genes from the PCCGs, firstly, the expression patterns of the 16 genes were examined in the hypothalamus of two indigenous breeds (LBS and Gushi (GS) chickens) between the pre-laying and peak-laying stages using quantitative real-time PCR (qRT-PCR).  Eleven out of the 16 genes showed significantly differential expression (P<0.05) with the same changing trends in the two breeds.  Then, correlations between the expression levels of the above 11 genes and egg numbers and reproductive hormone concentrations in serum were investigated in high-yielding and low-yielding GS chickens.  Of the 11 genes, eight showed significant correlations (P<0.05) between their expression levels and egg numbers, and between expression levels and reproductive hormone concentration in serum.  Furthermore, an association study on single nucleotide polymorphisms (SNPs) identified in these eight genes and egg production traits was carried out in 640 GS hens, and a significant association (P<0.05) between the SNPs and egg numbers was confirmed.  In conclusion, the eight genes, including CNR1, AP2M1, NRXN1, ANXA5, PENK, SLC1A2, SNAP25 and TRH, were demonstrated as key genes regulating egg production in indigenous chickens, and the SNPs sites within the genes might be served as markers to provide a guide for indigenous chicken breeding.  These findings provide a novel insight for further understanding the regulatory mechanisms of egg-laying performance and developing molecular markers to improve egg production of indigenous breeds.

OVATE family proteins (OFPs) are plant-specific proteins with a conserved OVATE domain that regulate plant growth and development.  Although OFPs have been studied in several species, their biological functions remain largely unknown in cucumber (Cucumis sativus L.).  This study identified 19 CsOFPs distributed on seven chromosomes in cucumber.  Most CsOFP genes were expressed in reproductive organs, but with different expression patterns.  Ectopic expression of CsOFP12-16c in Arabidopsis resulted in shorter and blunt siliques.  The overall results indicated that CsOFP12-16c regulates silique development in Arabidopsis and may have a similar function in cucumber.

MicroRNAs (miRNAs) are small (ca. 20–24 nucleotides) non-coding RNAs that have recently been recognized as key post-transcriptional modulators of gene expression; and they are involved in many biological processes in plants, such as root growth and development.  The miRNAs regulate root elongation, lateral root (LR) formation and adventitious root (AR) development in response to hormone signaling, nutrient uptake and biotic/abiotic stress.  This review provides multiple perspectives on the involvement of miRNAs in regulating root growth and development in plants.  We also discuss several crucial mechanisms of miRNAs, their relationships with transcription factors and the target gene-mediated hormone signaling interactions in the regulation of root growth and development.

Dopamine is a catecholamine and an anti-oxidant which functions in responses to stress and it interacts with plant hormones to mediate plant development.  At present, there are few studies on the functions of dopamine in apple.  This study developed a method for dopamine determination which was used to analyze dopamine in Malus germplasm, in order to clarify the tissue distribution, developmental changes, diurnal variations, and stress responses in apple trees.  First, the proposed method was verified.  The linear range of quantification was robust from 0.1 to 20 ng mL^–1.  The instrumental, inter-day precision, and sample repeatability relative standard deviations were 1.024, 5.607, and 7.237%, respectively.  The spiked recovery was greater than 100%, indicating the feasibility of the method and its suitability for the rapid analysis of dopamine in Malus.  Next, the dopamine content was measured in 322 Malus tissues.  The results showed that the dopamine level in Malus was low and the average dopamine content in leaf was higher than in peel and flesh.  The dopamine had a skewed distribution that deviated to the right in cultivars and wild accessions.  Finally, the tissue specificity, developmental changes, diurnal changes, and responses to stress were analyzed.  In cultivar ‘Pinova’ (Malus domestica), the dopamine concentration was the highest in leaf buds and lowest in flesh.  The dopamine contents in leaf and flesh decreased with the growth and development of cultivar ‘Liangxiang’ (Malus domestica).  The dopamine content of apple leaves was higher after either drought or salinity stress as compared to the control.  In this study, a dopamine detection method for apple was established based on HPLC-MS and shown to be a robust approach.  This study provides a framework for future research on elucidating the tissue distribution, developmental changes, diurnal variation, and stress responses of dopamine in apple trees.

Recent investigations on pomegranate products have significantly increased and successfully drawn consumers’ attention to nutritional and medicinal values, promoting the pomegranate industry’s development worldwide.  However, little information on pomegranates grown in China is available.  Morphological and chemical characterizations of fruits and arils from 20 pomegranate cultivars in six regions of China were investigated.  Combined with overall scores by principal component analysis, ‘Yushiliu No. 1’, ‘Taishanhong No. 2’, ‘Tunisia’ and ‘Mollar’ were promising cultivars, and Chinese researchers bred the first two.  It was surprising that ‘Mollar’ had bigger fruit size and more aril moisture grown in China than in Spain.  Cultivars with higher anthocyanin content in arils were ‘Turkey’, ‘Moyu’ and ‘Red Angel’, which might be used as the source of natural red food colourants.  While red husk ‘Hongruyi’ and ‘Hongshuangxi’ with higher vitamin C, aril moisture and lower titratable acid in arils, might also be promising cultivars for further various utilization.  Furthermore, the comparison of ‘Tunisia’ fruits from four regions revealed that cultivation locations had more influence on fruit traits than genotypes.  Maturity index classification was established for Chinese pomegranate cultivars.  Therefore, the results would provide a valuable guide for agricultural cultivation, industrial utilization, and breeding. 

Winter jujube (Ziziphus jujuba ‘Dongzao’) is an excellent late maturing variety of fresh-eating jujube in China.  Fruit texture is an important indicator of sensory quality.  To investigate the correlations among texture indices and establish an evaluation system for winter jujube texture, we used the TMS-Touch instrument to perform a texture profile analysis (TPA) on 1 150 winter jujubes from three major producing areas in China.  Eight indices and their best-fit distribution were obtained, including fracture (Pearson), hardness (InvGauss), adhesive force (Weibull), adhesiveness (LogLogistic), cohesiveness (LogLogistic), springiness (BetaGeneral), gumminess (InvGauss), and chewiness (InvGauss).  Based on the best-fit distribution curves, each index was divided into five grades (lower, low, medium, high and higher) by the 10th, 30th, 70th and 90th percentiles.  Among the texture indices, 82% of the correlation coefficients were highly significant (P<0.01); meanwhile, chewiness was significantly (P<0.01) and positively correlated with springiness and gumminess, of which the correlation coefficients were up to 0.8692 and 0.8096, respectively.  However, adhesiveness was significantly (P<0.01) and negatively related to adhesive force with a correlation coefficient of –0.7569.  Among hardness, cohesiveness, springiness, gumminess, and chewiness, each index could be well fitted by a multiple linear regression with the remaining four indices, with the coefficients above 0.94 and the mean fitting error and mean prediction error lower than 10%.  A comprehensive evaluation model was consequently established based on factor analysis to evaluate the texture quality of winter jujube.  The results demonstrated that winter jujube with higher comprehensive scores generally exhibited higher springiness and chewiness, but had lower adhesive force and adhesiveness.  We used factor analysis and clustering analysis to divide the eight studied texture into four groups (cohesive factor, adhesive-soft factor, tough-hard factor, and crispness factor), whose representative indices were springiness, adhesiveness, hardness, and fracture, respectively.  Overall, this study investigated the variation in each index of winter jujube texture, explored the association among these indices, screened the representative indices, and established a texture evaluation system.  The results provide a methodological basis and technical support for evaluating winter jujube texture.

Cell wall architecture plays a key role in stalk strength and forage digestibility.  Lignin, cellulose, and hemicellulose are the three main components of plant cell walls, and they can impact stalk quality by affecting the structure and strength of the cell wall.  To explore cell wall development during secondary cell wall lignification in maize stalks, conventional and conditional genetic mapping were used to identify the dynamic quantitative trait loci (QTLs) of the cell wall components and digestibility traits during five growth stages after silking.  Acid detergent lignin (ADL), cellulose (CEL), acid detergent fiber (ADF), neutral detergent fiber (NDF), and in vitro dry matter digestibility (IVDMD) were evaluated in a maize recombinant inbred line (RIL) population.  ADL, CEL, ADF, and NDF gradually increased from 10 to 40 days after silking (DAS), and then they decreased.  IVDMD initially decreased until 40 DAS, and then it increased slightly.  Seventy-two QTLs were identified for the five traits, and each accounted for 3.48–24.04% of the phenotypic variation.  Six QTL hotspots were found, and they were localized in the 1.08, 2.04, 2.07, 7.03, 8.05, and 9.03 bins of the maize genome.  Within the interval of the pleiotropic QTL identified in bin 1.08 of the maize genome, six genes associated with cell wall component biosynthesis were identified as potential candidate genes for stalk strength as well as cell wall-related traits.  In addition, 26 conditional QTLs were detected in the five stages for all of the investigated traits.  Twenty-two of the 26 conditional QTLs were found at 30 DAS conditioned using the values of 20 DAS, and at 50 DAS conditioned using the values of 40 DAS.  These results indicated that cell wall-related traits are regulated by many genes, which are specifically expressed at different stages after silking.  Simultaneous improvements in both forage digestibility and lodging resistance could be achieved by pyramiding multiple beneficial QTL alleles identified in this study.

Now, lodging is a major constraint factor contributing to yield loss of maize (Zea mays L.) under high planting density. Chemical regulation and nitrogen fertilizer could effectively coordinate the relationship between stem lodging and maize yield, which significantly reduce lodging and improve the grain yield. The purpose of this study was to explore the effects of chemical regulation and different nitrogen application rates on lodging characteristics, grain filling and yield of maize under high density. For this, we established a field study during 2017 and 2018 growing seasons, with three nitrogen levels of N100 (100 kg ha^–1), N200 (200 kg ha^–1) and N300 (300 kg ha^–1) at high planting density (90 000 plants ha^–1), and applied plant growth regulator (Yuhuangjin, the mixture of 3% DTA-6 and 27% ethephon) at the 7th leaf. The results showed that chemical control increased the activities of phenylalanine ammonia-lyase (PAL), tyrosine ammonia-lyase (TAL), 4-coumarate:CoA ligase (4CL), and cinnamyl alcohol dehydrogenase (CAD), and increased the lignin, cellulose and hemicellulose contents at the bottom of the 3rd internode, which significantly reduced the lodging percentage. The lignin-related enzyme activities, lignin, cellulose and hemicellulose contents decreased with the increase of nitrogen fertilizer, which significantly increased the lodging percentage. The 200 kg ha^–1 nitrogen application and chemical control increased the number, diameter, angle, volume, and dry weight of brace roots. The 200 kg ha^–1 nitrogen application and chemical control significantly increased the activities of ADP-glucose pyrophosphorylase (AGPase), soluble starch synthase (SSS) and starch branching enzyme (SBE), which promoted the starch accumulation in grains. Additional, improved the maximum grain filling rate (V_max) and mean grain filling rate (V_m), which promoted the grain filling process, significantly increased grain weight and grain number per ear, thus increased the final yield.

Northeast China (NEC) is one of the major maize production areas in China. Agro-climatic resources have obviously changed, which will seriously affect crop growth and development in this region. It is important to investigate the contribution of climate change adaptation measures to the yield and resource use efficiency to improve our understanding of how we can effectively ensure high yield and high efficiency in the future. In this study, we divided the study area into five accumulated temperature zones (ATZs) based on growing degree days (GDD). Based on the meteorological data, maize data (from agro-meteorological stations) and the validated APSIM-Maize Model, we first investigated the spatial distributions and temporal trends of maize potential yield of actual planted cultivars, and revealed the radiation use efficiency (RUE) and heat resource use efficiency (HUE) from 1981 to 2017. Then according to the potential growing seasons and actual growing seasons, we identified the utilization percentages of radiation (P_R) resource and heat resource (P_H) for each ATZ under potential production from 1981 to 2017. Finally, we quantified the contributions of cultivar changings to yield, P_R and P_H of maize. The results showed that during the past 37 years, the estimated mean potential yield of actual planted cultivars was 13 649 kg ha^–1, ranged from 11 205 to 15 257 kg ha^–1, and increased by 140 kg ha^–1 per decade. For potential production, the mean values of RUE and HUE for the actual planted maize cultivars were 1.22 g MJ^–1 and 8.58 kg (°C d)^–1 ha^–1. RUE showed an increasing tendency, while HUE showed a decreasing tendency. The lengths of the potential growing season and actual growing season were 158 and 123 d, and increased by 2 and 1 d per decade. P_R and P_H under potential production were 82 and 86%, respectively and showed a decreasing tendency during the past 37 years. This indicates that actual planted cultivars failed to make full use of climate resources. However, results from the adaptation assessments indicate that, adoption of cultivars with growing season increased by 2–11 d among ATZs caused increase in yield, P_R and P_H of 0.6–1.7%, 1.1–7.6% and 1.5–8.9%, respectively. Therefore, introduction of cultivars with longer growing season can effectively increase the radiation and heat utilization percentages and potential yield.

Chloroplasts are essential for plant photosynthesis and growth. Many genes have been identified that regulate plant chloroplast development. However, it is not known at a molecular level how these genes regulate chloroplast biogenesis. In this study, we isolated a mutant ygl2 (yellow-green leaf2) that exhibited a pigment-defective phenotype. YGL2 encodes a geranylgeranyl reductase, and in mutant ygl2, there was a single base change (T1361G) located in the third exon of YGL2 that resulted in a missense mutation (L454R) in the encoded product. Transmission electron microscopy revealed that chloroplast development was impaired in the ygl2 mutant. The expression levels of plastid-encoded genes were significantly altered in the ygl2 mutant. Furthermore, in a yeast two-hybrid assay, we found that YGL2 interacted with the RNA editing factor MORF8.