Search Results (51)

Although numerous quantitative trait loci (QTLs) and candidate genes have been implicated in litter size in certain pig breeds, the genetic basis underlying the pronounced differences in reproductive capacity among breeds remains incompletely understood. To elucidate the underlying mechanisms responsible for the heterogeneity in reproductive capacity, we performed integrated transcriptomic and metabolomic analyses on ovarian tissues from two pig breeds with contrasting litter sizes: Diannan Small-ear (DSE) pigs and Yorkshire (YK) pigs. YK pigs exhibited significantly higher total born piglets. Transcriptome analysis revealed that upregulated DEGs in YK ovaries were enriched in ovarian steroidogenesis, retinol metabolism, vitamin digestion/absorption, and folate biosynthesis. In contrast, DSE pigs showed enrichment in inflammatory and immune-related pathways. Furthermore, integrative transcriptomic and metabolomic analysis revealed that upregulated DEGs in YK pigs, such as STAR and COL3A1, and concurrently elevated metabolites (e.g., L-threonine, L-asparagine, L-proline, L-methionine, arachidonic acid, and progesterone) were jointly enriched in three key pathways: protein digestion and absorption, mineral absorption, and aldosterone synthesis and secretion. These genes and metabolites are implicated in granulosa cell and oocyte proliferation, maturation, and protection against oxidative damage. Our findings provide a theoretical foundation for future strategies aimed at improving reproductive performance through targeted modulation of key genes and metabolites. Full article

Maize (Zea mays L.) is the most extensively cultivated food crop in China, and current studies on maize general combining ability (GCA) focus primarily on the genetic basis of traits. However, the dynamic trends and underlying genetic loci associated with GCA for yield-related traits during breeding remain underexplored. This study was designed to investigate the changing trends of the general combining ability (GCA) and the frequency of elite alleles among 218 major maize inbred lines from Northeast China, spanning the 1970s to the 2010s. PH6WC and PH4CV were used as testers to develop 436 hybrid combinations via the North Carolina design II (NCII) method, and these combinations were evaluated across three environments. We further analyzed the combining ability (particularly the GCA) of 16 yield-related traits and their dynamic trends during breeding, grouped into three age periods (AGE1: 1960s–1970s; AGE2: 1980s–1990s; AGE3: 2000s–2010s). We also screened for genetic loci associated with the GCA effects of these traits. Results show that breeding selection significantly affected the GCA of six yield-related traits (ear length (EL), tassel branch number (TBN), tassel main axis length (TL), kernel length (KL), stem diameter (SDR), and hundred kernel weight (HKW)). Specifically, the mean TBN_GCA value decreased from 2.51 in AGE1 to −1.28 in AGE3, and the mean HKW_GCA increased from −1.58 in AGE1 to 0.36 in AGE3. Yield per plant GCA (YPP_GCA) was positively correlated with the GCA values of EL, ear diameter (ED), kernel row number (KRN), kernel number per row (KNPR), and HKW. Association analysis identified 38 single nucleotide polymorphisms (SNP_S) related to GCA. The T/T alleles for TBN were absent in AGE1, emerged in AGE2 (1980s–1990s), and persisted in AGE3—consistent with the decreasing trend of TBN_GCA from AGE1 to AGE3. For HKW, the A/A alleles not only exhibited higher GCA (effectively improving the HKW_GCA of inbred lines) but also showed an 11% increase in allelic frequency from AGE1 to AGE3. Taken together, these results suggest that the accumulation of elite alleles is the primary factor driving the GCA improvement during maize breeding in Northeast China. Full article

Yield components are the most important breeding objectives, directly determining maize high-yield breeding. It is well known that these traits are controlled by a large number of quantitative trait loci (QTL). Therefore, deeply understanding the genetic basis of yield components and identifying key regulatory candidate genes can lay the foundation for maize marker-assisted selection (MAS) breeding. In this study, our aim was to identify the key genomic regions that regulate maize yield component formation through bioinformatic methods. Herein, 554 original QTLs related to 11 yield components, including ear length (EL), hundred-kernel weight (HKW), ear weight (EW), cob weight (CW), ear diameter (ED), cob diameter (CD), kernel row number (KRN), kernel number per row (KNR), kernel length (KL), grain weight per plant (GW), and kernel width (KW) in maize, were collected from the MaizeGDB, national center for biotechnology information (NCBI), and China national knowledge infrastructure (CNKI) databases. The consensus map was then constructed with a total length of 7154.30 cM. Approximately 80.32% of original QTLs were successfully projected on the consensus map, and they were unevenly distributed on the 10 chromosomes (Chr.). Moreover, 44 meta-QTLs (MQTLs) were identified by the meta-analysis. Among them, 39 MQTLs controlled two or more yield components, except for the MQTL4 in Chr. 1, which was associated with HKW; MQTL11 in Chr. 2, which was responsible for EL; MQTL19 in Chr. 3, which was related to KRN; MQTL26 in Chr. 5, which was involved in HKW; and MQTL36 in Chr. 7, which regulated EL. These findings were consistent with the Pearson correlation results, indicating that these traits exhibited co-linked heredity phenomena. Meanwhile, 159 candidate genes were found in all of the above MQTLs intervals, of which, 29 genes encoded E3 ubiquitin protein ligase, which was related with kernel size and weight. Other genes were involved in multiple metabolic processes, including plant hormones signaling transduction, plant growth and development, sucrose–starch synthesis and metabolism, and reproductive growth. Overall, the results will provide reliable genetic resources for high-yield molecular breeding in maize. Full article

Agronomic advancements have led to significant increases in maize yield per hectare in Northeast China, primarily through improved density tolerance. However, the genetic mechanism underlying grain yield responses to density stress remains poorly understood. Here, a population of 193 recombinant inbred lines (RILs) derived from the cross between ZM058 and PH1219 was employed to identify quantitative trait loci (QTLs) under two planting densities across three locations over two years. Six yield-related traits were investigated: ear tip-barrenness length (BEL), cob diameter (CD), ear diameter (ED), ear length (EL), kernel number per row (KNR), and kernel row number (KRN). These traits exhibited distinct and divergent responses to density stress, with the values of CD, ED, EL, KNR and KRN decreasing as planting density increased, except for BEL. A total of 81 QTLs were identified for these traits: 39 were unique to low planting density, 22 to high planting density, and 20 were shared across both conditions. Additionally, nine QTL clusters implicated in the development of multiple traits were detected. The results indicate that planting density significantly affects yield traits, primarily through the interaction of numerous minor QTLs with multiple effects. This insight enhances our understanding of the genetic basis of yield-related traits and provides valuable guidance for breeding high-density-tolerant varieties. Full article

Drought severely limits crop yield every year, making it critical to clarify the genetic basis of drought tolerance for breeding of improved varieties. As drought tolerance is a complex quantitative trait, we analyzed three phenotypic groups: (1) agronomic traits under well-watered (WW) and water-deficit (WD) conditions, (2) stress tolerance indices of these traits, and (3) phenotypic plasticity, using a multi-parent doubled haploid (DH) population assessed in multi-environment trials. Genome-wide association studies (GWAS) identified 130, 171, and 71 quantitative trait loci (QTL) for the three groups of phenotypes, respectively. Only one QTL was shared among all trait groups, 25 between stress indices and agronomic traits, while the majority of QTL were specific to their group. Functional annotation of candidate genes revealed distinct pathways of the three phenotypic groups. Candidate genes under WD conditions were enriched for stress response and epigenetic regulation, while under WW conditions for protein synthesis and transport, RNA metabolism, and developmental regulation. Stress tolerance indices were enriched for transport of amino/organic acids, epigenetic regulation, and stress response, whereas plasticity showed enrichment for environmental adaptability. Transcriptome analysis of 26 potential candidate genes showed tissue-specific drought responses in leaves, ears, and tassels. Collectively, these results indicated both shared and independent genetic mechanisms underlying drought tolerance, providing novel insights into the complex phenotypes related to drought tolerance and guiding further strategies for molecular breeding in maize. Full article

Background: Crossbreeding strategies that combine the growth performance of Western pig breeds with the meat quality traits of Chinese indigenous breeds have garnered considerable interest. Duroc pigs are known for their high growth efficiency but have relatively low intramuscular fat (IMF) content. In contrast, native breeds like the Diannan Small-Eared pig exhibit superior pork quality with higher IMF levels. This study aimed to compare the muscle growth characteristics and molecular mechanisms between Duroc × Landrace × Yorkshire (DLY) and Duroc × Berkshire × Diannan Small-Eared (DBD) pigs. Methods: The longissimus dorsi tissue of 210-day-old DLY and DBD pigs was collected for analysis. HE staining assessed muscle fiber characteristics, IMF content was measured, and ELISA quantified muscle-derived growth and development-related factors. Transcriptome sequencing was conducted, followed by differential gene expression analysis, Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and protein–protein interaction (PPI) analyses. Functional validation of key genes was performed in C2C12 cells. Results: DBD pigs exhibited significantly larger muscle fiber diameter and higher IMF content compared to DLY pigs. IGF1 and GH levels were elevated in DBD pigs. Transcriptome analysis identified 185 upregulated and 102 downregulated genes, with enrichment in pathways including PI3K-Akt, MAPK, FoxO, and cGMP-PKG signaling. ACSL1 and FABP3 were functionally validated, showing promotion of differentiation and inhibition of proliferation in C2C12 cells. Conclusions: DBD pigs exhibit superior muscle growth traits and higher IMF content compared to DLY pigs. ACSL1 and FABP3 may serve as key regulators of muscle development in pigs. Full article

Oat (Avena sativa L.) is one of the most important self-fertilizing field plants belonging to the Poaceae family. It has no significant requirements regarding growing conditions but has a very good reaction to fertilization. The current research evaluated the significance of the effects of individual applications of mineral (NPK) and organo-mineral (OMF) fertilizers, as well as their individual combination with slaked lime (calcium hydroxide, Ca(OH)₂), on the yield, morphological traits [mean number of leaves per plant—MNLP, minimum leaf length (cm) per plant—MinLL, maximum leaf length (cm) per plant—MaxLL, number of ears per plant—NEP], and physiological parameters (nitrogen balance index—NBI, content of chlorophyll—Chl, flavonoids—Flv, anthocyanins—Ant) of organic and pelleted (graded) oat plants, comparing the treatments and in relation to the control. The experiment was performed in semi-controlled glasshouse conditions, in pots, from the fourth week of March to the fourth week of June 2024, using Vertisol soil. This soil is characterized as light clay with an acid reaction. Physiological parameters were measured using a Dualex leaf clip sensor. The results obtained showed that physiological parameters in both oat types significantly differed (p < 0.05) between the treatments applied and in relation to the control, whereas the morphological traits did not significantly differ (p > 0.05) between the treatments. Statistically significant differences (p < 0.05) in the yield of both oat types were most pronounced in the OMF + Slaked Lime treatment (organic: 4.49 g pot⁻¹; pelleted: 4.61 g pot⁻¹) in relation to the control (organic: 2.48 g pot⁻¹; pelleted: 2.63 g pot⁻¹). The pelleted oats showed slightly better results for the effects of different treatments across all tested parameters compared to organic oats. In conclusion, the best results were obtained with the use of OMF + Slaked Lime, which could be proposed as the optimal fertilization treatment for pelleted and organic oat cultivation based on this research. Full article

Germplasm improvement is essential for maize breeding. Currently, intra-heterotic-group crossing is the major method for germplasm improvement, while inter-heterotic-group crossing is also used in breeding but not in a systematic way. In this study, five inbred lines from four heterotic groups were used to develop a connected segregating population through inter-heterotic-group line crossing (CSPIC), which comprised 5 subpopulations with 535 doubled haploid (DH) lines and 15 related test-cross populations including 1568 hybrids. Significant genetic variation was observed in most subpopulations, with several DH populations exhibiting superior phenotypes regarding traits such as plant height (PH), ear height (EH), days to anthesis (DTA), and days to silking (DTS). Notably, 10.8% of hybrids in the population POP5/C229 surpassed the high-yielding hybrid ND678 (CK). To reduce field planting costs and quickly screen for the best inter-heterotic-group DH lines and test-cross hybrids, we assessed the accuracy of genomic selection (GS) for within- and between-population predictions in the DH populations and the test-cross populations. Within the DH or the hybrid population, the prediction accuracy varied across populations and traits, with an average hybrid yield prediction accuracy of 0.41, reaching 0.54 in POP5/Z58. In the cross DH population predictions, the prediction accuracy of the half-sib population exceeded that of the non-sib cross population prediction, with the highest accuracy observed when the non-shared parents were from the same heterotic group, and the average phenotypic prediction accuracies of POP3 predicting POP2 and POP2 predicting POP3 were 0.54 and 0.45, respectively. In the cross hybrid population predictions, the accuracy was highest when both the training and the test sets came from the same DH populations, with an average accuracy of 0.43. The proportion of shared polymorphisms with respect to SNPs between the training and the test sets (PSP) exhibited a significant and strong correlation with the prediction accuracy of cross population prediction. This study demonstrates the feasibility of creating new heterotic groups through inter-heterotic-group crossing in germplasm improvement, and some cross population prediction patterns exhibited excellent prediction accuracy. Full article

Assessing genetic gains from historical data provides insights to improve breeding programs. This study evaluated the Mozambique National Maize Program’s (MNMP’s) genetic gains using data from advanced germplasm trials conducted at 21 locations between 2014 and 2020. Genetic gains were calculated by regressing the genotypic best linear unbiased estimates of grain yield and complementary agronomic traits against the initial year of genotype evaluation (n = 592). The annual genetic gain was expressed as a percentage of the trait mean. While grain yield, the primary breeding focus, showed no significant improvement, significant gains were observed for the plant height (0.67%), ear height (1.74%), ears per plant (1.31%), ear position coefficient (1.22%), and husk cover (4.7%). Negative genetic gains were detected for the days to anthesis (−0.5%), the anthesis–silking interval or ASI (−9.31%), and stalk lodging (−5.01%). These results indicate that while MNMP did not achieve the desired positive genetic gain for grain yield, progress was made for traits related to plant resilience, particularly the ASI and stalk lodging. MNMP should seek to incorporate new breeding technologies and human resources to enhance genetic gains for grain yield and other key traits in the maize breeding program, while developing and deploying high-yielding, climate-resilient maize varieties to address emerging food security challenges in Mozambique. Full article

Maize is a critical crop for food, feed, and bioenergy worldwide. This study characterized the genetic diversity and population structure of 212 important inbred lines collected from the Southeast China breeding program using the Maize6H-60K single nucleotide polymorphism (SNP) array. To investigate the genetic architecture of plant height (PH) and ear height (EH), genome-wide association analysis (GWAS) was performed on this population in 2021 and 2022. Cluster analysis and population genetic structure analysis grouped the 212 maize inbred lines into 10 distinct categories. GWAS identified significant associations for PH, EH, and the EH/PH ratio. A total of 40 significant SNP (p < 8.55359 × 10⁻⁷) were detected, including nine associated with PH, with phenotypic variation explained (PVE) ranging from 3.42% to 25.92%. Additionally, 16 SNP were linked to EH, with PVE ranging from 2.49% to 38.49%, and 15 SNP were associated with the EH/PH ratio, showing PVE between 3.43% and 16.83%. Five stable SNP, identified across two or more environments, were further analyzed. Three of these SNP loci are reported for the first time in this study: two loci associated with the PH, AX-108020973, and AX-108022922, as well as one new locus, AX-108096437, which was significantly associated with the EH/PH ratio. Additionally, two other significant SNP (AX-247241325 and AX-108097244) were located within a 2 Mb range of previously identified QTL and/or related SNP. Within the 200 kb confidence intervals of these five stable SNP loci, 76 functionally annotated genes were identified. Further functional analysis indicated that 14 of these genes may play a role in regulating plant morphology, which is primarily involved in hormone synthesis, microtubule development, root growth, and cell division regulation. For instance, the homologous genes GRMZM2G375249 and GRMZM2G076029 in maize correspond to OsPEX1 in rice, a protein similar to extension proteins that are implicated in lignin biosynthesis, plant growth promotion, and the negative regulation of root growth through gibberellin-mediated pathways. The candidate gene corresponding to AX-108097244 is GRMZM2G464754; previous studies have reported its involvement in regulating EH in maize. These findings enhance the understanding of QTL associated with maize plant-type traits and provide a foundation for cloning PH, EH-related genes. Therefore, the results also support the development of functional markers for target genes and the breeding of improved maize varieties. Full article

The mass of nutrients accumulated in the vegetative parts of winter wheat (WW) in the period from the beginning of booting to the full flowering stage (Critical Cereal Window, CCW) allows for the reliable prediction of the grain yield (GY) and its components, and the grain protein content (GPC) and its yield. This hypothesis was verified in a one-factor field experiment carried out in the 2013/2014, 2014/2015, and 2015/2016 growing seasons. The field experiment included seven nitrogen-fertilized variants: 0, 40, 80, 120, 160, 200, and 240 kg N ha⁻¹. The N, P, K, Ca, Mg, Fe, Mn, Zn, and Cu content in wheat vegetative parts (leaves, stems) was determined in two growth stages: (i) beginning of booting (BBCH 40) and (ii) full flowering (BBCH 65). We examined the response of eight WW traits (ear biomass at BBCH 65, EAB; grain yield, GY; grain protein content, GPC; grain protein yield, GPY; canopy ear density, CED; number of grains per ear, GE; number of grains per m⁻²—canopy grain density, CGD; and thousand grain weight, TGW) to the amount of a given nutrient accumulated in the given vegetative part of WW before flowering. The average GY was very high and ranged from 7.2 t ha⁻¹ in 2016 to 11.3 t ha⁻¹ in 2015. The mass of ears in the full flowering stage was highest in 2016, a year with the lowest GY. The highest N mass in leaves was also recorded in 2016. Only the biomass of the stems at the BBCH 65 stage was the highest in 2015, the year with the highest yield. Despite this variability, 99% of GY variability was explained by the interaction of CGD and TGW. Based on the analyses performed, it can be concluded that in the case of large yields of winter wheat, GE is a critical yield component that determines the CGD, and in consequence the GY. The leaf nutrient mass at the BBCH 40 stage was a reliable predictor of the GPC (R² = 0.93), GPY (0.92), GE (0.84), and CED (0.76). The prediction of the GY (0.89), CGD (0.90), and TGW (0.89) was most reliable based on the leaf nutrient mass at the BBCH 65 stage. The best EAB prediction was obtained based on the mass of nutrients in WW stems at the BBCH 65 stage. The magnesium accumulated in WW parts turned out to be, with the exception of TGW, a key predictor of the examined traits. In the case of the TGW, the main predictor was Ca. The effect of Mg on the tested WW traits most often occurred in cooperation with other nutrients. Its presence in the developed stepwise regression models varied depending on the plant part and the WW trait. The most common nutrients accompanying Mg were micronutrients, while Zn, Fe, Mn, and Ca were the most common macronutrients accompanying Mg. Despite the apparently small impact of N, its yield-forming role was indirect. Excessive N accumulation in leaves in relation to its mass in stems, which appeared in the full flowering phase, positively impacted the EAB and GPC, but negatively affected the GE. Increasing the LE/ST ratio for both Mg and Ca resulted in a better formation of the yield components, which, consequently, led to a higher yield. This study clearly showed that nutritional control of WW during the CCW should focus on nutrients controlling N action. Full article

Inconsistent reports exist on the relationships between key agronomic traits and maize yield. We performed a multivariate analysis of yield and 10 agronomic traits in 59 hybrids to explore maize yields in mountainous areas. The yield per plant (YP) was significantly and positively correlated with kernel weight (KW), growth period (GP), and kernel row number (KRN). KW and KRN had positive effects on YP, whereas kernel rows per ear (KRE) had a negative effect. GP indirectly affected YP. GP, KW, KRN, and ear length (EL) showed the highest grey relational degree with YP. The first four principal components cumulatively accounted for 73.36% of variation. EL, KW, plant height (PH), ear height (EH), GP, KRN, and YP contributed positively to the variation, whereas KRE, shelling percentage (SP), bald-tip length (BTL), and ear girth (EG) contributed negatively. Based on trait similarity, the 59 maize hybrids were classified into two clusters, Clusters I and II. A total of 11 traits were grouped into four clusters, Clusters A–D. Cluster D included KW, GP, KRN, EL, EH, PH, and YP, and the 22 maize hybrids in Cluster I performed better in these traits. These results provide a theoretical basis for the breeding of high-yield maize varieties in mountainous areas. Full article

Leaf angle (LA) is a major agronomic trait of rice plant architecture, which is determined by the development of the leaf lamina joint (LJ) and closely related to plant yield. The LJ is formed by the leaf collar belt (ligule band), leaf tongue (ligule) and leaf ear (auricle). Parenchyma cells (PCs), sclerenchyma cells (SCs), vascular bundles (VBs), and arenchyma tissue (Ac) are present in the cross sections of LJ. The genetic and molecular regulation of rice leaf angle and LJ development has been well investigated in recent years. However, the underlying complex regulatory network still requires further elucidation and comprehensive discussion. In this review, we briefly describe the cellular characteristics of four typical stages of LJ development, and systematically summarize the genes regulating rice leaf inclination based on their roles in PC proliferation and elongation, as well as SC proliferation and differentiation. We also introduce the emerging regulatory pathways of phytohormones and transcription factors (TFs), environmental cues that are involved in rice LJ development, discussing the relevant intricate signal network that is relevant to provide further insights into the genetic improvement of leaf angle traits in rice breeding. Full article

Nitrogen is an essential element for maize growth, but excessive application can lead to various environmental and ecological issues, including water pollution, air pollution, greenhouse gas emissions, and biodiversity loss. Hence, developing maize hybrids resilient to low-N conditions is vital for sustainable agriculture, particularly in nitrogen-deficient soils. Combining ability and genetic relationships among parental lines is crucial for breeding superior hybrids under diverse nitrogen levels. This study aimed to assess the genetic diversity of maize inbred lines using simple sequence repeat (SSR) markers and evaluate their combining ability to identify superior hybrids under low-N and recommended conditions. Local and exotic inbred lines were genotyped using SSR markers, revealing substantial genetic variation with high gene diversity (He = 0.60), moderate polymorphism information content (PIC = 0.54), and an average of 3.64 alleles per locus. Twenty-one F1 hybrids were generated through a diallel mating design using these diverse lines. These hybrids and a high yielding commercial check (SC-131) were field-tested under low-N and recommended N conditions. Significant variations (p < 0.01) were observed among nitrogen levels, hybrids, and their interaction for all recorded traits. Additive genetic variances predominated over non-additive genetic variances for grain yield and most traits. Inbred IL3 emerged as an effective combiner for developing early maturing genotypes with lower ear placement. Additionally, inbreds IL1, IL2, and IL3 showed promise as superior combiners for enhancing grain yield and related traits under both low-N and recommended conditions. Notably, hybrids IL1×IL4, IL2×IL5, IL2×IL6, and IL5×IL7 exhibited specific combining abilities for increasing grain yield and associated traits under low-N stress conditions. Furthermore, strong positive associations were identified between grain yield and specific traits like plant height, ear length, number of rows per ear, and number of kernels per row. Due to their straightforward measurability, these relationships underscore the potential of using these traits as proxies for indirect selection in early breeding generations, particularly under low-N stress. This research contributes to breeding nitrogen-efficient maize hybrids and advances our understanding of the genetic foundations for tolerance to nitrogen limitations. Full article

The wheat grain yields increased in EU from 4.98 t ha⁻¹ to 5.45 t ha⁻¹ in the periods from 2006 to 2014 to from 2015 to 2023. It is hypothesized that changes in specific morphological traits over the years resulted in grain yield increase due to the utilization of new wheat varieties in production. To highlight the current status and changes over time, we evaluated a comprehensive panel of 1322 wheat varieties that included testing of morphological traits of varieties recognized from period from 2006 till 2023. Positive relation of registration year with traits such as seed color, glaucosity of neck of culm, plant height, ear length, scurs and awns length, ear color, and shape of the beak of the lower glume was obtained. The most significant changes over time resulted in a darker color of the seed, decreased area of hairiness of the convex surface of the apical rachis segment, enhanced glaucosity of the neck of the culm and decreased frequency of the plants with recurved flag leaves. It was shown that traits such as the frequency of plants with recurved flag leaves, time of emergence, glaucosity of flag leaves, existence of scurs and awns, and area of the hairiness of the convex surface of the apical rachis segment had significant decreases over time. This research demonstrated the importance of twelve morphological traits in the varietal improvement of grain yield over the time from 2006 to 2023. Full article