Mitochondria and chloroplast are very important organelles for organism, participating in basic life activity. Their genomes contain many repeats which can lead to a variation of genome structure. Oryza is an important genus for human beings’ nutrition. Several mitochondrial and chloroplast genomes of Oryza have been sequenced, which help us to insight the distribution and evolution of the repeats

β-glucan is an important trait to be improved in barley breeding programs, as it greatly affects the quality of the end products when barley grains are used as raw material of feed or malt production or consumed as food for human. Although the genes associated with β-glucan synthesis have been identified, genetic regulation of β-glucan accumulation in barley grains is still completely unclear. In this

Plant height (PH) is closely associated with yield-related traits and environmental adaptation. Seven pairs of near-isogenic lines (NILs) targeting four QTL on 3AL, 4BL, 4AS, and 7AL wheat chromosome arms were assessed for PH and four yield-related traits including yield per plant (Y/P), grain number per spike (G/S), thousand kernel weight (TKW), and biomass per plant (B/P). Significant differences

Brassica juncea is an important economic crop of the world; however, the narrow genetic base of this crop has tremendously decreased its crop productivity. As an ancestral species of B. juncea, B. nigra is of great importance in widening the genetic diversity of B. juncea. In the present study, 42 SSR markers were employed to screen the genetic diversity among 83 B. nigra, 16 B. juncea, and other Brassica

The uses of vegetable oils are determined by functional properties arising from their chemical composition. Soybean oil was previously used in margarines and baked foods after partial hydrogenation to achieve heat and oxidative stability. This process, however, generates trans fats that are now excluded from food use because of cardiovascular health risks. Also present in soybean oil are the anti-oxidant

Maize (Zea mays) is a leading cereal crop in the world. The maize kernel is the storage organ and the harvest portion of this crop and is closely related to its yield and quality. The development of maize kernel is initiated by the double fertilization event, leading to the formation of a diploid embryo and a triploid endosperm. The embryo and endosperm are then undergone independent developmental

Elucidation of the genomic organizations of transgene insertion sites is essential for the genetic studies of transgenic plants. Herein, we establish an analysis pipeline that identifies the transgene insertion sites as well as the presence of vector backbones, through de novo genome assembly with high-throughput sequencing data in two transgenic soybean lines, AtYUCCA6-#5 and 35S-UGT72E3/2-#7. Sequencing

Good eating quality is a highly desirable trait of rice which determines its commercial value and market share. However, the molecular basis of this trait remains largely unknown. Here, three high-quality conventional rice cultivars, including two superior eating quality cultivars Meixiangzhan-2 (MXZ) and Xiangyaxiangzhan (XYXZ), and one ordinary eating quality cultivar Huanghuazhan (HHZ), were analyzed

Maize (Zea mays L.) is an important crop around the world, but its growth and production can be severely limited by waterlogging. In response to waterlogging stress, elaborate regulatory mechanisms have evolved in maize under both natural and artificial selection. Some research efforts involving genetic, genomic, and molecular strategies have focused on waterlogging stress biology in maize. Waterlogging

Zinc (Zn) is an essential micronutrient for human, and improving Zn concentration in rice could be a simple and effective way to solve insufficient Zn uptake from daily diet. In this study, a recombinant inbred line (RIL) population was developed from a commercial hybrid combination Wandao153, and subjected to quantitative trait loci (QTL) detection for Zn concentration in brown rice and heading date

Developing new population types based on interspecific introgressions has been suggested to facilitate the discovery of novel allelic sources for traits of agronomic importance. In this study, a chromosome segment substitution line (CSSL) rice population carrying contiguous chromosomal segments of japonica Nipponbare in the genetic background of indica 9311 was developed. Meanwhile, a high-density

The present study showed that exogenous abscisic acid (ABA) pre-treatment remarkably increases the freeze tolerance of common wheat (Triticum aestivum L.) seedlings at the anther connective tissue formation phase (ACFP) and tetrad developmental phase. After 3-day freeze stress, ABA pre-treatment significantly increases the content of soluble sugar, soluble protein, and proline, activities of superoxide

ALK is the key gene of controlling rice gelatinization temperature (GT), and at least three ALK alleles are thought to be responsible for the diversity of GT among rice cultivars. But whether the sequence polymorphism of the promoter region also associated with GT is not clearly studied. In this study, we analyzed sequence variation in the promoter region of ALK and mainly two types of promoter were

Gray leaf spot (GLS) disease, caused by the Stemphylium (Sm) fungus, affects a wide range of horticultural crops including tomato. In this study, the South Korean Sm isolate (PNU-SM01) was identified, and the applicability of Sm-resistance gene (Sm)-linked DNA markers in marker-assisted selection was validated. ITS/gpd sequencing and morphological observation identified the isolate as S. lycopersici

In recent years, rice false smut (RFS) has grown from being a minor to a major disease affecting rice productivity. The genetic basis of the host’s defense against RFS is currently under-researched. In this study, a rice variety Nanjing11 with stable resistance to RFS from years under naturally infected field condition was identified. The genetic analysis showed that the RFS resistance of Nanjing11

Wheat (Triticum aestivum L.) is a major staple crop in East Africa (EA) providing 9% and 10% of daily calories and protein intake, respectively. However, EA countries depend on import to meet 55% of their domestic wheat supplies due to increasing demands and low domestic yields. To determine the beneficial gene pool currently exploited for wheat improvement in EA, we examined the allelic diversity

High β-glucan content is one of the main goals of oat breeding programs worldwide. However, the genomic regions and genes controlling β-glucan content in oats are not fully understood. In this sense, the objectives of this study were as follows: (i) to characterize structure and linkage disequilibrium (LD) in a panel of oat germplasm adapted to subtropical environments; and (ii) to identify genomic

The Editor-in-Chief has retracted this article [1] at the request of the first and last author. Following publication, the first and last author have stated that the quantitative real-time PCR (qPCR) analysis was outsourced to a third party.

Hybrid sterility is a major obstacle to the development of superior inter-subspecific hybrids between indica and japonica subspecies of Asian-cultivated rice. To overcome hybrid sterility, we introduced four japonica alleles (S-j) at Sa, Sc, f5, and S32 loci from Nipponbare into 9311 through marker-assisted backcross breeding, and four improved lines were obtained. Three wide-compatibility lines 9311(S5-n)

As the second most destructive disease in soybean (Glycine max (L.) Merr), Phytophthora root or stem-rot (PRR) of soybean, which was caused by Phytophthora sojae (P. sojae), could lead to a 10–40% or complete yield loss annually. Researches were needed to perform to identify the P. sojae-resistant germplasm and to better understand the genetic basis of P. sojae resistance in soybean. A total of 225

As soybean is highly sensitive to photoperiod, and the cultivation area of soybean is restricted to a narrow latitude region. The adaptability of soybean growth across wide latitude areas is owing to the rich variations of genes conditioning the flowering time and maturity. Identification of new quantitative trait loci (QTLs) and validation of the potential genes are beneficial to clarify the complex

Cotton is not only a natural fiber crop, but also an important economic crop in China. The cultivation of cotton with longer, stronger, and finer fiber has been the goal of cotton breeders. Germin-like proteins (GLPs) is a group of protein family with cupin domain, which mainly acts as an enzyme. However, the function of GLPs involved in regulating cotton fiber development is rarely understood. Here

The generation of transgenic floricultural crops for flower color modification requires a transgene that enhances anthocyanin accumulation and a flower-specific promoter with stable expression throughout flowering stage. Here, the anthocyanin regulatory R2R3-MYB transcription factor (TF) RsMYB1 was placed under the control of the stable flower-specific promoter (InMYB1) to enhance anthocyanin accumulation

Rapeseed (Brassica napus) is an important oil crop that supplies a considerable amount of global vegetable oil production. Genetic transformation system is important to gene functional analysis and molecular breeding. Here, an efficient Agrobacterium-mediated transformation protocol using hypocotyl of rapeseed as explants is described. To develop this protocol, we compared several essential factors

Brown planthopper (BPH) is one of the most destructive pests in rice. Breeding resistant cultivars is the most effective strategy to control BPH. Bph3 is a broad-spectrum and durable BPH resistance locus spanning ~ 50 kb on the short arm of rice chromosome 4. Using the genomic variation data of 4726 rice varieties from public database, we developed 8 InDel markers within the Bph3 locus. By analyzing

Gibberella ear rot (GER), caused by the fungal pathogen Fusarium graminearum, is becoming one of the most prominent pathogens responsible for ear rot in maize. In this study three F2 populations, F2-C, F2-D, and F2-J, and their corresponding F2:3 families, were constructed by crossing three highly GER-resistant inbred lines—Cheng351, Dan598, and JiV203—with the susceptible line ZW18. We used this cross

The quantitative trait locus SD1-2 for seed dormancy (SD) is identical to the semi-dawrf1 (sd1) gene prevailing in high-yield varieties of rice. However, sd1 alone appeared not sufficient to overcome the preharvest sprouting (PHS) problem in crop (or hybrid seed) production. This research aimed to address some genetic issues that may impact pyramiding of SD genes to improve semi-dwarf varieties for

Northern corn leaf blight (NCLB) is one of the main diseases of maize, which greatly reduces production and causes millions of dollars in losses worldwide annually. Identification of NCLB resistance genes in maize plays an important role in the crop disease resistance breeding. In this study, a BC1F1 population with 1290 individuals was constructed using high resistance line CML493 and high susceptible

Gibberella ear rot (GER) caused by Fusarium graminearum (teleomorph Gibberella zeae), is one of the most devastating diseases in maize that not only severely reduces grain yield but also contaminates the kernels with potent mycotoxins which is harmful to livestock and humans. Identification of stable quantitative trait loci (QTL) and candidate genes conferring resistance is a promising strategy in

Male reproductive development is vital for crop seed production. However, the mechanism underlying remains largely unknown. Here, we isolated a male sterile mutant osgelp34-1 in rice. Cytological analysis indicated that the mutant exhibited delayed degradation of anther wall layers and abnormal pollen development, which resulted in the production of shrunk and non-viable pollen grains. MutMap and CRISPR/Cas9

Late blight is a disease with the biggest economic impact on potato cultivation worldwide. Pyramiding of the resistance genes originating from potato wild relatives is a breeding strategy that has a potential to produce potato cultivars durably resistant to late blight. Growing such cultivars would allow limiting the intensive chemical control of the disease. The goal of this work was to transfer the

Rice (Oryza sativa L.) in Japan is not only a food staple but also an important material for the Japanese alcoholic beverage, sake. The grain used in sake brewing has different characters from the cooking rice grain, including a large grain size and high white-core expression rate (WCE). Because large-sized grains often have a heavy grain weight and higher yield, this trait is also important for cooking

Soybean is an important crop used for oil production. Alterations of the fatty acids, especially increased oleic acid content, can improve the nutritional quality and oxidative stability of soybean oil. During seed development, two genes, encoding FAD2-1A and FAD2-1B, are mainly responsible for the transformation from oleic acid to linoleic acid, and the combination of fad2-1a and fad2-1b is the key

The Spanish local cultivar ‘Ambrunés’ stands out due to its high organoleptic quality and fruit firmness. These characteristics make it an important parent for breeding cherries with excellent fresh and post-harvest quality. In this work, an F1 sweet cherry population (n = 140) from ‘Ambrunés’ × ‘Sweetheart’ was phenotyped for 2 years for fruit diameter, weight and firmness and genotyped with the RosBREED

In this study, we performed a transcriptomic analysis to investigate genome-wide gene profiles of a rapeseed (Brassica napus) cultivar Zhongshuang 11 (ZS11) in response to waterlogging stress at germination stage. The root and shoot development of ZS11 was dramatically inhibited by waterlogging stress. As a result, 7472 downregulated DEGs (differentially expressed genes) and 3869 upregulated DEGs were

The Green Revolution of the 1960s introduced semi-dwarf cultivars of rice that had reduced lodging and increased harvest indexes. The mutant allele of Semi Dwarf 1 (SD1) is the gene underlying the Green Revolution advances in rice yield. Since that time, most of the commercial semi-dwarf cultivars carry a mutation in SD1. Unlike japonica rice cultivars containing weak functional SD1 alleles, indica

Improving the nitrogen use efficiency (NUE) may considerably increase maize yield and decrease the use of nitrogen (N) fertilizer. But the genetic basis of NUE in maize is still poorly understood. In this study, an association panel of 139 maize inbred lines genotyped with 50,790 single nucleotide polymorphism (SNP) was used to dissect the genetic basis of NUE-related traits by genome-wide association

Lack of seed dormancy, a major cause of pre-harvest sprouting in rice and other cereal crops, causes significant reductions in grain yield and quality. Weedy rice is often strongly dormant; therefore, quantitative trait loci (QTLs) related to seed dormancy in weedy rice “Ludao” could be useful for improving pre-harvest sprouting resistance in the important japonica variety “Ninggeng 4.” To identify

Most wheat cultivars planted worldwide are susceptible to the stem rust Ug99 race group. To prepare for the potential spread of these races into South America, we aimed to identify genomic regions responsible for resistance to Ug99 race group in germplasm adapted to South America. Two RIL populations from a cross between a stem rust susceptible parent “Baguette 13” and resistant local parents “INIA

As over-fertilization leads to environmental concerns, selecting cultivars that can produce high yields on phosphorus (P)-deficient soils and understanding the genetic basis underlying P-starved tolerance have become crucially important. In this study, we evaluated the variation of ten P deficiency-related traits at the seedling stage of 419 core accessions in two different environments. The results

Disease resistance in Brassica juncea has been shown against several diseases including blackleg, white rust, hypocotyl rot, turnip mosaic virus, leaf blight, black rot, and Alternaria blight. The identification of disease resistance genes is important to develop elite cultivars, which can survive exposure to these diseases. The largest family of resistance genes are nucleotide-binding site leucine-rich

Plant height is the important determinant for the yield formation of rice, and selecting of an optimal plant height is necessary during rice breeding to achieve ideal biomass and lodging resistance. In this study, allele variation of Sd1, the well-known “green revolution” gene, was clarified as the major factor for plant height segregation in the breeding populations from an indica and japonica cross

The original article unfortunately contains mistake.

A rice hybrid is the product of a cross between two genetically distinct inbred lines. Owing to yield heterosis in rice hybrids, hybrid rice breeding has been developed and widely used in agriculture. In some cases, the hybrid F1 lines show extremely late flowering. However, the genetic basis of the phenomenon is not very clear. In this study, two hybrids were found to have heading date of ~ 130 days

The low seedling rate of rice caused by submergence in the process of rice direct seeding has always been an important factor limiting the popularization of rice direct seeding technology. Improving the tolerance of rice to submergence stress will benefit the production of rice and the promotion of direct seeding technology. In this study, we determined the submergence coleoptile length (SCL), submergence

Seed yield is one of the main limitations in hybrid rice production. The improvement of stigma exsertion rate (SER) of male sterility lines is essential for the higher seed yield in hybrid rice. Wild rice species are valuable germplasms with exserted stigma. It is worthy of mining-related genes for SER in wild rice species, as well as probing the way to use the beneficial genes in rice breeding. In

Forage sorghum (Sorghum bicolor (L.) Moench) is a wildly cultivated C4 cereal crop in many geographical regions and differs among germplasms in a number of important physiological traits. Lignin is a complex heteropolymer found in plant cell walls that adversely affects economic and environmental benefits of the crop. To understand the genetic basis, we re-sequenced the genomes of 206 sorghum accessions

Brassinosteroids (BRs) are a class of plant-specific steroid hormones and play an essential role in plant growth and development. The DWARF4 (DWF4) gene encodes a C-22 hydroxylase, which is a rate-limiting enzyme in BR biosynthesis pathway. Here, the DWF4 (ZmDWF4) in maize (Zea mays L.), the ortholog of Arabidopsis DWF4 (CYP90B1), was transformed into elite inbred Q319 and driven maize ubiquitin promoter

Unfortunately, in the final version of this article the original Table 6 was not included in the proofing step and the Table 5 was duplicated.

Soybean mosaic virus (SMV) threatens soybean (Glycine max (L.) Merr.) production and seed quality worldwide. Host plant resistance is the most environmentally friendly and economically effective method to deduce the damages of SMV. However, the use of limited resistant loci in SMV management will be conquered due to SMV strain shifts caused by evolutionary arms races. Thus, exploration of novel germplasms

Thousand grain weight (TGW) is one of the three crucial determinants of wheat (Triticum aestivum) grain yield. The identification of functional genes and development of closely linked markers are urgently needed for wheat yield improvements. In this study, quantitative trait locus (QTL) mapping for TGW was carried out using one RIL population in four environments. A total of 8 QTL controlling TGW were

Kernel width (KW) is a key determinant of kernel weight and an important selection trait during the maize domestication and improvement. KW is a complex quantitative trait that is controlled by many quantitative trait loci (QTL) with minor effects, but the underlying genes for KW using natural variation remain rarely reported in maize. In this study, using advanced backcross populations from the cross

Three gene promoters from the model legume species Medicago truncatula and Medicago sativa (alfalfa) pathogenesis-related (PR) proteins (MtPR5, MtPR10, and MsPR10) were isolated and investigated using in silico and in situ approaches. For the functional analysis of these promoters, plant transformation vectors linking promoter sequences with the β-glucuronidase (GUS) reporter gene were constructed

To identify genes associated with genic male sterility (GMS) that are useful for hybrid breeding in Brassica crops, we analyzed the “ms77B” strain, which is a spontaneous turnip GMS mutant derived from a cv. 77B population. Previously, we reported that the GMS phenotype of ms77B is caused by a single gene with sterility as the recessive trait. To identify the causative gene of GMS in ms77B, we performed

The introduction of semi-dwarf cereal crop varieties in the 1960s enabled extensive increases in global food production. Semi-dwarf barley cultivars have shorter stature and improved stress resistance, grain yield and quality than tall varieties. The major semi-dwarf genes, sdw1 and ari-e, have been widely used in barley breeding programmes worldwide. In this study, we identified a novel sdw1 allele

Plant aquaporins (AQPs) are subdivided into eight groups: PIPs, NIPs, GIPs, HIPs, XIPs, LIPs, TIPs, and SIPs. However, the genetic function and physiological mechanisms of the SIP group in abiotic stress response in plants remains unknown. In this study, we cloned and characterized a banana SIP group AQP gene, designated MaSIP2-1. MaSIP2-1 showed upregulation after osmotic, salt, and cold treatments

Meloidogyne graminicola is one of the most important plant-parasitic nematodes in rice. Breeding for natural resistance and tolerance is considered one of the most economical and sustainable approaches to control this damaging pathogen. Quantitative trait loci (QTL) mapping was carried out in a recombinant inbred line (RIL) population derived from a cross between the Asian rice genotypes IR78877-208-B-1-2

Male sterile lines are important for hybrid seed production in Brassica rapa. In our previous study, we obtained a multiple-allele inherited male sterile line of Chinese cabbage. To identify the male sterile gene Ms in B. rapa, we used B. rapa L. var. chinensis (‘AB03’; MsMs) and B. rapa var. purpuraria (‘AB04’; MsfMsf) as parents to construct an F2 segregating population, and mapped the Ms gene on

Pod number is an important component of yield in soybean (Glycine max (L.) Merr.), and pods are unevenly distributed in the upper, middle and lower parts of the plant. Here, linkage analysis combined with genome-wide association study (GWAS) was used to identify 20 pod number-related traits in four-way recombinant inbred lines (FW-RILs) derived from crosses between the four soybean varieties (Kenfeng

Gray leaf spot (GLS), caused by the fungal pathogen Cercospora zeae-maydis, is one of the most serious foliar diseases of maize worldwide. In the present study, a population of recombinant inbred lines (RILs) derived from a gray leaf spot–resistant inbred line Qi319 and a susceptible line Ye478 was used to map quantitative trait loci (QTL) for GLS resistance. For initial QTL analysis, genetic maps