Breeding semi-dwarf cultivars has long been a major objective for wheat improvement due to the inseparable association between plant height (PH) and grain yield. Although the utilization of Rht-B1b and Rht-D1b genes successfully achieved semi-dwarfism in the 1960s, these genes were associated with undesirable traits. The current wheat breeding urgently requires continuously exploring PH-controlling genes and their regulatory mechanisms, which will expand the genetic diversity of the PH gene pool to achieve precise PH regulation while maintaining or even increasing the grain yield potential. In this study, we identified a gibberellin (GA)-sensitive dwarf mutant, designated wph3 (wheat plant height 3). It showed GA biosynthesis deficiency and had pleiotropic effects on PH, spike length, grain weight, and grain number per spike. Using Exome Capture Sequencing for Bulked Segregant Analysis and molecular marker mapping, a novel recessive nuclear dwarfing gene was identified and localized into a 3.9 Mb physical interval on chromosome 2B, designated Rht29 (Reduced height 29). Transcriptome analysis and candidate gene mining indicated that Rht29 may not encode a canonical key enzyme for GA biosynthesis, but participate in the GA biosynthesis by regulating the expression level of GA3ox. This study enriches the genetic resources available for wheat dwarfing breeding and establishes a foundation for further molecular characterization of phenotypic regulation by Rht29.

Peanut (Arachis hypogaea L.) is an important oilseed crop whose yield is threatened by various abiotic stresses. Glycosyltransferases are crucial for diverse plant functions, including the regulation of plant growth and development, biotic and abiotic stress response, and the biosynthesis of secondary metabolites. However, the mechanism of glycosyltransferases relates to abiotic stresses remains unclear in peanut. In this study, we isolated a novel gene, AhIRX7, from a salt-tolerant mutant of peanut. The expression of AhIRX7 was strongly induced by NaCl and PEG6000. Overexpression of AhIRX7 led to increased, whereas silenced of AhIRX7 resulted in decreased tolerance of peanut seedlings to salt and drought stresses. Compared to wild-type (WT), the overexpression lines showed significantly increased chlorophyll fluorescence parameters and reduced photodamage under salt and drought stress. Their activities of superoxide dismutase (SOD), peroxidase (POD) and catalase (CAT) were markedly enhanced, while the accumulation of superoxide anion (O2−), hydrogen peroxide (H2O2) and malondialdehyde (MDA) were significantly reduced. In contrast, AhIRX7-silenced lines exhibited opposite trends in SOD, POD, and CAT activities, as well as MDA accumulation. Consequently, overexpression of AhIRX7 improved the regulation of photosynthesis, the dynamics of stomatal opening and closing under salt and drought stress in Arabidopsis plants. Overall, this study indicated that AhIRX7 gene functions in enhancing drought and salt stresses in peanuts and Arabidopsis, which may serve as a candidate gene for use in improving abiotic stress resistance in crops.

Peanut (Arachis hypogaea L.), a vital oilseed and cash crop, faces yield limitations due to abiotic stresses. The 9-cis-epoxycarotenoid dioxygenase (NCED) enzyme, a key enzyme in abscisic acid (ABA) biosynthesis regulating plant development and stress responses, remains mechanistically uncharacterized in peanut abiotic stress tolerance. In this study, we isolated a novel gene, AhNCED4, from the salt-tolerant mutant M24. The expression of AhNCED4 was strongly induced by NaCl, PEG6000, and ABA in peanut huayu20. Overexpression of AhNCED4 enhanced salt and drought tolerance in Arabidopsis. Transgenic overexpression of AhNCED4 improved salt and stress resistance through upregulated ROS-scavenging genes superoxide dismutase (SOD), peroxidase (POD), and catalase (CAT) with elevated enzymatic activities while reducing malondialdehyde (MDA), superoxide anion (O2-), and hydrogen peroxide (H2O2) accumulation compared to wild-type plants. Further research showed that the chlorophyll fluorescence parameters of transgenic lines were significantly increased, while light damage was significantly reduced. These findings establish AhNCED4 as a critical regulator of stress adaptation and an excellent candidate gene for resistance breeding in peanut.

Leaf senescence is a turning point for grain development and closely related to yield and grain quality. Fine-tuning leaf senescence could be a vital strategy for yield improvement. However, our knowledge of the regulatory genes of leaf senescence is limited in wheat. In this study, we identified a methanesulfonate (EMS) mutant, wheat pale green 1 (wpg1), exhibiting obvious leaf chlorisis and premature senescence (PS) since the jointing stage. The chloroplast structure of the chlorisis leaf of wpg1 seemed intact, whereas its chlorophyll content was significantly decreased compared to the wild type (WT). The content of nitrogen (N), the core element for chlorophyll, was much lower in leaves of wpg1 than in WT. The spatio-temporal pattern analysis of nitrogen content further indicated accelerated N allocation from vegetation tissues to spike in wpg1, resulting in a significant decrease in nitrogen content in leaves, but a substantial increase in grains compared to WT. Genetic analysis showed that leaf chlorisis and PS is controlled by a single dominant locus, designated as Wheat Pale Green 1 (WPG1), which was further mapped to a physical interval of 34.69 M-41.19 M on chromosome 2A. Transcriptomic analysis revealed that expression of photosynthesis-related genes, and N absorption and transportation genes consistently decreased in wpg1, which revalidated the underlying relationship between N shortage and leaf chlorisis. The results presented here lays the basis for further dissecting the causal gene of WPG1 and the subsequent molecular mechanism underlying the regulation of leaf senescence, N allocation, and possibly the photosynthesis in wheat.

AhRt3, which governs the red testa of peanut, was narrowed down to a 125.30 kb region, and one gene encoding anthocyanin reductase was identified as the putative candidate gene. Testa color is a special characteristic of peanuts (Arachis hypogaea L.), and those with dark testa have been focused on recent years owing to their high-anthocyanin content and increased antioxidant nutritional value. However, the genetic mechanisms underlying this trait remain limited. To identify the gene responsible for the red testa color in peanuts, an F2 population was constructed by crossing YH91 (pink testa) with JHT1 (red testa). Genetic analysis revealed that the red testa was controlled by a single dominant gene named AhRt3 (Arachis hypogaea Red Testa 3). Through bulked segregant analysis sequencing, AhRt3 was preliminarily mapped to the chromosome Arahy.03 and subsequently narrowed to a 125.30 kb genomic region containing 12 potential candidate genes. RNA-seq analysis revealed that 4,880 genes were differentially expressed in the seed testa, with only the candidate gene Arahy.W8TDEC exhibiting higher expression levels in JHT1 than in YH91. Additionally, sequence variation, functional annotation, and expression profiling confirmed that Arahy.W8TDEC, which encodes an anthocyanin reductase, may be a candidate gene for AhRt3. The structural variation involving an inversion between the sixth exon and the 3’UTR of Arahy.W8TDEC resulted in altered amino acids closely associated with the red testa phenotype in peanuts. In conclusion, this study highlights the role of a novel gene in regulating red testa and contributes valuable insights into the genetic basis of seed testa in peanuts.

BACKGROUND:Plant height (PH), as a key trait of plant architecture, is the embodiment of biomass accumulation and plays a critical role in determining wheat yield. Excavating diverse PH genes and understanding their pleiotropic effects on important agronomic traits are essential to enrich the PH gene pool and facilitate their further application in breeding. RESULTS:In this study, five stable PH QTLs were identified on chromosome 2B, 4A, 4B, 5A and 6A in a double haploid (DH) population from the cross between two elite wheat cultivars, Chuanmai 42 and Kechengmai 1. The QPh.cib-4B and QPh.cib-6A were major QTL and had a significant additive effect on PH. The QPh.cib-4B was confirmed as the Rht-B1, and QPh.cib-6A might be a new QTL. The major QTLs were further validated in different genetic backgrounds using the Kompetitive Allele-Specific PCR (KASP) markers. Using near-isogenic lines (NILs), QPh.cib-6A was demonstrated to pleiotropically increase plant height (PH), thousand grain weight (TGW), and spike length (SL) without negatively affecting grain number per spike (GNS) or spikelet number per spike (SNS). In contrast, QPh.cib-4B exhibited significant effects on PH but had no influence on TGW, GNS, SL, or SNS. Notably, the frequency of elite haplotype of QPh.cib-6A remains relatively low in Chinese wheat varieties. Thus, the combination of QPh.cib-4B and QPh.cib-6A represents a promising genetic module with considerable potential for high-yield wheat breeding. Expression analysis in NILs and sequence characterization identified TraesCS6A02G234400 and TraesCS6A02G235300 as the candidate genes for QPh.cib-6A. CONCLUSIONS:This study identified five QTLs for PH in wheat. Two major QTLs were further validated in different genetic backgrounds, and their genetic effects on yield-related traits were analyzed in near-isogenic lines (NILs) to evaluate their potential in wheat breeding. Taken together, our results advance our understanding of the genetic basis for PH and enrich the PH QTL pool. CLINICAL TRIAL NUMBER:Not applicable.

Seven stable QTLs for TGW, GW and GL were identified, and two major QTLs were stable in various genetic backgrounds and environments. Thousand grain weight (TGW), mainly determined by grain length (GL) and width (GW), is an important yield component of wheat. In the study, combined with phenotyping in four field trials and a high-quality genetic map constructed with the wheat 55 K SNP array, a total of seven stable QTLs for TGW, GW and GL were identified in a doubled haploid (DH) population derived from the cross between Chuanmai 42 (CM42) and Kechengmai 4 (K4), in which QTgw.CK4-cib-3D, QGw.CK4-cib-2D and QGl.CK4-cib-5 A.1 were novel, and QTgw/Gw.CK4-cib-6 A and QGl.CK4-cib-5 A.1 were major QTLs explaining more than 10

A major locus for spike compactness and length was mapped on chromosome 7H and its pleiotropic effects, candidate genes and transcriptional regulatory network were analyzed. Spike compactness (SC) and length (SL) are important traits of barley (Hordeum vulgare L.) due to their close association with grain yield. In this study, a major SC and SL locus QSc/Sl.cib-7H was primarily identified on chromosome 7H by bulked segregant analysis, and further fine mapped to a recombination cold spot expanding 244.36–388.09 Mb by developing a secondary population using residual heterozygous lines. This region is much more accurate than previously reported spike compactness loci on chromosome 7H. The strong effects of QSc/Sl.cib-7H on SL and SC were validated in two pair of near isogenic lines (NILs) and diverse genetic backgrounds. QSc/Sl.cib-7H exhibited pleiotropic effects on plant height (PH), thousand grain weight and grain length, and did not significantly influence the spikelet number of main spike (SMS) and grain width. Transcriptome analysis based on NILs showed that regulation of SC and SL might be related to the plant circadian rhythm pathway. The candidate genes were mined by analyzing variants and expression patterns of genes in the target region employing multiple genome and transcriptome data. This study takes a further step towards cloning of QSc/Sl.cib-7H, and the data obtained and the developed molecular markers will facilitate its utilization in barley breeding.

Spike-related traits and plant height (PH) are greatly associated with wheat yield. Identification of stable quantitative trait loci (QTL) for these traits is crucial for understanding the genetic basis for yield and their further application in breeding. In this study, QTL analysis for spikelet number per spike (SNS), spike length (SL), spike compactness (SC) and PH was performed using a recombinant inbred line (RIL) population derived from a cross between wheat cultivars Mianmai902 (MM902) and Taichang29 (TC29). Thirteen stably expressed QTLs were identified, and the most favorable alleles were contributed by MM902. The mjaor QTL, QSNS-MT.cib-2D, QSL-MT.cib-2D, QSC-MT.cib-2D, QSC-MT.cib-6 A, QPH-MT.cib-4B and QPH-MT.cib-4D, were repeatedly detected in multiple environments and explained 5.77-47.11

Ethylene plays essential roles in plant growth, development and stress responses. The ethylene signaling pathway and molecular mechanism have been studied extensively in Arabidopsis and rice but limited in peanuts. Here, we established a sand-culture method to screen pingyangmycin mutagenized peanut lines based on their specific response to ethylene (“triple response“). An ethylene-insensitive mutant, inhibition of peanut hypocotyl elongation 1 (iph1), was identified that showed reduced sensitivity to ethylene in both hypocotyl elongation and root growth. Through bulked segregant analysis sequencing, a major gene related to iph1, named AhIPH1, was preliminarily mapped at the chromosome Arahy.01, and further narrowed to a 450-kb genomic region through substitution mapping strategy. A total of 7014 genes were differentially expressed among the ACC treatment through RNA-seq analysis, of which only the Arahy.5BLU0Q gene in the candidate mapping interval was differentially expressed between WT and mutant iph1. Integrating sequence variations, functional annotation and transcriptome analysis revealed that a predicated gene, Arahy.5BLU0Q, encoding SNF1 protein kinase, may be the candidate gene for AhIPH1. This gene contained two single-nucleotide polymorphisms at promoter region and was more highly expressed in iph1 than WT. Our findings reveal a novel ethylene-responsive gene, which provides a theoretical foundation and new genetic resources for the mechanism of ethylene signaling in peanuts

ACC oxidase (ACO) is one of the key enzymes that catalyze the synthesis of ethylene. Ethylene is involved in salt stress response in plants, and salt stress seriously affects the yield of peanut. In this study, AhACO genes were cloned and their functions were investigated with the aim to explore the biological function of AhACOs in salt stress response, and to provide genetic resources for the breeding of salt-tolerant varieties of peanut. AhACO1 and AhACO2 were amplified from the cDNA of salt-tolerant peanut mutant M29, respectively, and cloned into the plant expression vector pCAMBIA super1300. The recombinant plasmid was transformed into Huayu22 by pollen tube injection mediated by Agrobacterium tumefaciens. After harvest, the small slice cotyledon was separated from the kernel, and the positive seeds were screened by PCR. The expression of AhACO genes was analyzed by qRT-PCR, and the ethylene release was detected by capillary column gas chromatography. Transgenic seeds were sowed and then irrigated with NaCl solution, and the phenotypic changes of 21-day-seedings were recorded. The results showed that the growth of transgenic plants were better than that of the control group Huayu 22 upon salt stress, and the relative content of chlorophyll SPAD value and net photosynthetic rate (Pn) of transgenic peanuts were higher than those of the control group. In addition, the ethylene production of AhACO1 and AhACO2 transgenic plants were 2.79 and 1.87 times higher than that of control peanut, respectively. These results showed that AhACO1 and AhACO2 could significantly improve the salt stress tolerance of transgenic peanut.

有性杂交是花生(Arachis hypogaea L.)育种的重要途径,真杂种鉴定对于遗传群体的构建以及新品种选育至关重要.花生含油量的表型鉴定极易受到环境条件的影响,且目前缺少可用的分子标记.本研究选用高油及普通油酸亲本宇花14号与低油及高油酸亲本LOP215杂交构建含油量相关遗传群体.宇花14号含有AhFAD2A及AhFAD2B位点,基因型为AABB,LOP215含有AhFAD2a及AhFAD2b位点,基因型为aabb.以宇花14号为母本、LOP215为父本杂交,收获F1杂交籽仁,采用竞争性等位基因特异性PCR(Kompetitive Allele Specific PCR,KASP)检测AhFAD2基因型,剔除AhFAD2基因型为纯合的籽仁,选留FAD2基因型为杂合的F1真杂种.F1真杂种单粒播种收获后,单株检测含油量,对于F2表型无明显分离的株系,取各单株叶片等量混合后提取DNA,进行AhFAD2基因型检测再次确认AhFAD2位点的杂合性.经二次验证后的F2籽粒经连续自交6代后选育出包含460个家系的重组自交系(recombinant inbred lines,RIL)群体,其含油量呈连续正态分布,可作为含油量基因定位的有效分离群体.本试验以AhFAD2作为选择标记能简单高效地筛选出真杂种,构建目标性状分离群体,为花生含油量基因定位及高低油花生品种选育提供材料.

Additional file 18: Supplementary table 8.

为加强黄河三角洲盐碱地的开发利用,扩大花生种植面积,提高花生产量,本研究以17份花生品种(系)为材料,利用水培方法,测定不同盐浓度下萌发期发芽率.确定0.7％NaCl浓度作为花生品种萌发期耐盐性鉴定的最适浓度,共筛选出5个耐盐品种(系).在山东平度非盐碱地和东营盐碱地分别种植5个耐盐和4个非耐盐品种(系),测定产量性状相关指标.结果表明,盐碱胁迫显著降低花生发芽率,明显抑制花生的生长发育和产量.高油酸品种宇花18号表现出较强的耐盐碱性,其次是化学诱变突变体品系ST24-1、ST24-8和ST24-11,均适于盐碱地种植,为耐盐碱花生品种的选育提供了新材料.本研究表明,萌发期耐盐性的鉴定可作为花生耐盐碱鉴定的基础指标之一.

Background Yield-related traits including thousand grain weight (TGW), grain number per spike (GNS), grain width (GW), grain length (GL), plant height (PH), spike length (SL), and spikelet number per spike (SNS) are greatly associated with grain yield of wheat ( Triticum aestivum L.). To detect quantitative trait loci (QTL) associated with them, 193 recombinant inbred lines derived from two elite winter wheat varieties Chuanmai42 and Chuanmai39 were employed to perform QTL mapping in six/eight environments. Results A total of 30 QTLs on chromosomes 1A, 1B, 1D, 2A, 2B, 2D, 3A, 4A, 5A, 5B, 6A, 6D, 7A, 7B and 7D were identified. Among them, six major QTLs QTgw.cib-6A.1 , QTgw.cib-6A.2 , QGw.cib-6A , QGl.cib-3A , QGl.cib-6A , and QSl.cib-2D explaining 5.96-23.75% of the phenotypic variance were detected in multi-environments and showed strong and stable effects on corresponding traits. Three QTL clusters on chromosomes 2D and 6A containing 10 QTLs were also detected, which showed significant pleiotropic effects on multiple traits. Additionally, three Kompetitive Allele Specific PCR (KASP) markers linked with five of these major QTLs were developed. Candidate genes of QTgw.cib-6A.1/QGl.cib-6A and QGl.cib-3A were analyzed based on the spatiotemporal expression patterns, gene annotation, and orthologous search. Conclusions Six major QTLs for TGW, GL, GW and SL were detected. Three KASP markers linked with five of these major QTLs were developed. These QTLs and KASP markers will be useful for elucidating the genetic architecture of grain yield and developing new wheat varieties with high and stable yield in wheat.

Peanut ( Arachis hypogaea L.) is an important crop used for oil production, and oleic acid is a major factor in determining oil quality. Alterations in the oleic acid content can improve the nutritional quality and oxidative stability and prolong the shelf life of peanut products. The objective of this study was to develop a peanut variety with a high-oleic-acid content and high yield. One elite variety, “huayu22,” was hybridized with the high-oleic-acid “KN176” donor and backcrossed for four generations as the recurrent parent using fad2 marker-assisted backcross selection. Based on the Kompetitive allele-specific PCR (KASP) screening of fad2 markers, the oleic acid content of advanced generations derived by selfing was assessed by near-infrared reflectance spectroscopy and gas chromatography. The genetic background recovery rate of four BC 4 F 4 lines showed an average of 92.34% and was confirmed by genotyping using the Axiom_ Arachis 58 K SNP array. Across these superior lines in BC 4 F 6 generations, one line with a high-oleic-acid content and high yield was detected and named “YH61.” In particular, yield comparison experiments showed that YH61 exhibited high and stable yield at three different locations and was moderately resistant to leaf spot disease. The distinctness, uniformity and stability (DUS) testing for two consecutive years suggested that YH61 reached the standard for variety rights application. The use of the peanut variety YH61 contributed to the expansion of the cultivation area due to its high value in the oleic acid market and the proven economic benefits in China. This study demonstrated that the marker-assisted backcross strategy based on a cost-effective KASP assay and SNP array for the detection of mutations in fad2 and genetic background evaluation can be used to create efficient peanut breeding programs and contribute to oil quality and high-yield stability.

Auxin response factors (ARFs) are transcription factors that regulate the transcription of auxin-responsive genes during plant growth and development. In this study, 29 and 30 ARF members were identified from the two wild peanut species, A. duranensis and A. ipaensis, respectively. The ARFs, including their classifications, conserved domains and evolutionary relationships were characterized. RNA-seq analyses revealed that some of the ARF genes were responsive to abiotic stress, particularly high salinity. In addition to abiotic stress, the expression of 2 ARF members was also regulated by biotic stress, specifically Bradyrhizobium infection in A. duranensis. The ARF gene Arahy.7DXUOK was predicted to be a potential target of miR160. Overexpression of miR160 could cause degradation of the Arahy.7DXUOK target gene transcript and increased salt tolerance in miR160OX transgenic plants. Therefore, these molecular characterization and expression profile analyses provide comprehensive information on ARF family members and will help to elucidate their functions to facilitate further research on peanuts.

Background The cultivated peanut ( Arachis hypogaea L., AABB) is an allotetraploid hybrid between two diploid peanuts, A. duranensis (AA genome) and A. ipaensis (BB genome). Miniature inverted-repeat transposable elements (MITEs), some of which are known as active nonautonomous DNA transposons with high copy numbers, play important roles in genome evolution and diversification. AhMITE1 , a member of the MITE family of transposons, but information on the peanut genomes is still limited. Here, we analyzed AhMITE1 , AuMITE1 and ApMITE1 in the cultivated ( A. hypogaea ) and two wild peanut ( A. duranensis and A. ipaensis ) genomes. Results The cultivated and the two wild peanut genomes harbored 142, 14 and 21 AhMITE1 , AuMITE1 and ApMITE1 family members, respectively. These three family members exhibited highly conserved TIR sequences, and insertions preferentially occurred within 2 kb upstream and downstream of gene-coding and AT-rich regions. Phylogenetic and pairwise nucleotide diversity analysis showed that AhMITE1 and ApMITE1 family members have undergone one round of amplification bursts during the evolution of the peanut genome. PCR analyses were performed in 23 peanut varieties and demonstrated that AhMITE1 is an active transposon and that hybridization or chemical mutagenesis can promote the mobilization of AhMITE1 . Conclusions AhMITE1 , AuMITE1 and ApMITE1 family members were identified based on local BLAST search with MAK between the cultivated and the two wild peanut genomes. The phylogenetic, nucleotide diversity and variation copy numbers of AhMITE1 , AuMITE1 and ApMITE1 members provides opportunities for investigating their roles during peanut evolution. These findings will contribute to knowledge on diversity of AhMITE1 , provide information about the potential impact on the gene expression and promote the development of DNA markers in peanut.

Morphological, genetic and transcriptomic characterizations of an EMS-induced wheat paired spikelets (PS) mutant were performed. A novel qualitative locus WPS1 on chromosome 1D was identified. Grain yield of wheat is significantly associated with inflorescence or spike architecture. However, few genes related to wheat spike development have been identified and their underlying mechanisms are largely unknown. In this study, we characterized an ethyl methanesulfonate (EMS)-induced wheat mutant, wheat paired spikelets 1 (wps1). Unlike a single spikelet that usually develops at each node of rachis, a secondary spikelet appeared below the primary spikelet at most of the rachis nodes of wps1. The microscope observation showed that the secondary spikelet initiated later than the primary spikelet. Genetic analysis suggested that the PS of wps1 is controlled by a single dominant nuclear gene, designated WHEAT PAIRED SPIKELETS 1 (WPS1). Further RNA-seq based bulked segregant analysis and molecular marker mapping localized WPS1 in an interval of 208.18–220.92 Mb on the chromosome arm 1DL, which is different to known genes related to spike development in wheat. By using wheat omics data, TraesCS1D02G155200 encoding a HD-ZIP III transcription factor was considered as a strong candidate gene for WPS1. Transcriptomic analysis indicated that PS formation in wps1 is associated with auxin-related pathways and may be regulated by networks involving TB1, Ppd1, FT1, VRN1, etc. This study laid the solid foundation for further validation of the causal gene of WPS1 and explored its regulatory mechanism in PS formation and inflorescence development, which may benefit to kernel yield improvement of wheat based on optimization or design of spike architecture in the future.