Identification of NADPH Oxidase Genes Crucial for Rice Multiple Disease Resistance and Yield Traits.

Reactive oxygen species (ROS) act as a group of signaling molecules in rice functioning in regulation of development and stress responses. Respiratory burst oxidase homologues (Rbohs) are key enzymes in generation of ROS. However, the role of the nine Rboh family members was not fully understood in rice multiple disease resistance and yield traits. In this study, we constructed mutants of each Rboh genes and detected their requirement in rice multiple disease resistance and yield traits. Our results revealed that mutations of five Rboh genes (RbohA, RbohB, RbohE, RbohH, and RbohI) lead to compromised rice blast disease resistance in a disease nursery and lab conditions; mutations of five Rbohs (RbohA, RbohB, RbohC, RbohE, and RbohH) result in suppressed rice sheath blight resistance in a disease nursery and lab conditions; mutations of six Rbohs (RbohA, RbohB, RbohC, RbohE, RbohH and RbohI) lead to decreased rice leaf blight resistance in a paddy yard and ROS production induced by PAMPs and pathogen. Moreover, all Rboh genes participate in the regulation of rice yield traits, for all rboh mutants display one or more compromised yield traits, such as panicle number, grain number per panicle, seed setting rate, and grain weight, resulting in reduced yield per plant except rbohb and rbohf. Our results identified the Rboh family members involved in the regulation of rice resistance against multiple pathogens that caused the most serious diseases worldwide and provide theoretical supporting for breeding application of these Rbohs to coordinate rice disease resistance and yield traits.

Effects of Straw Mulching on Soil Properties and Enzyme Activities of Camellia oleifera-Cassia Intercropping Agroforestry Systems.

In order to explore the influences of rice straw mulching on soil fertility in agroforestry systems, the soil C and N contents and enzyme activities were investigated in a C. oleifera-cassia intercropping ecosystem in Central Southern China. Three straw mulching application treatments were set up in this study, in 2021, namely, straw powder mulching (SPM), straw segment mulching (SSM), and non-straw mulching as the control (CK). Soil samples were collected from three soil depths (0-10 cm,10-20 cm, and 20-40 cm) in each treatment on the 90th-day after the treatments. The soil organic carbon (SOC), total nitrogen (TN), microbial carbon (MBC), soil enzyme activities (including acid phosphatase (ACP), urease (UE), cellulase (CL), and peroxidase (POD)), and soil water content (SWC) were determined. The results showed that the SOC significantly increased due to the mulching application in SPM and SSM, in the topsoil of 0-10 cm when compared to the CK. The SWC, SOC, TN, and MBC increased by 0.8 and 56.5, 3.5 and 37.5, 21.3 and 61.6, and 5.8% and 76.8% in the SPM and SSM treatments compared to the CK, respectively. The soil enzyme activities of ACP, UE, CE, and POD increased significantly due to straw mulching compared with CK throughout all soil layers. The soil enzyme activities of CL and POD were significantly higher in SSM than in SPM across the soil depth except for ACP. The enzyme activities of ACP were 14,190, 12,732, and 6490 U/g in SSM, SPM, and control, respectively. This indicated that mulching application enhanced the enzyme activity of ACP. Mulching had no significant effects on UE and CL, while the POD decreased significantly in the order of SPM > SSM > CK across all soil layers, being, on average, 6.64% and 3.14% higher in SSM and SPM, respectively, compared to the CK plots. The SOC and MBC were the key nutrient factors affecting the soil enzyme activities at the study site. The results from this study provided Important scientific insights for improving soil physicochemical properties during the management of the C. oleifera intercropping system and for the development of the C. oleifera industry.

Soil Nutrients, Enzyme Activities, and Microbial Communities along a Chronosequence of Chinese Fir Plantations in Subtropical China.

Forests undergo a long-term development process from young to mature stages, yet the variations in soil nutrients, enzyme activities, microbial diversity, and community composition related to forest ages are still unclear. In this study, the characteristics of soil bacterial and fungal communities with their corresponding soil environmental factors in the young, middle, and mature stages (7, 15, and 25-year-old) of Chinese fir plantations (CFP) in the subtropical region of China were investigated in 2021. Results showed that the alpha diversity indices (Chao1 and Shannon) of soil bacteria and fungi were higher in 15 and 25-year-old stands than in 7-year-old stand of CFP, while the soil pH, soil water content, soil organic carbon, total nitrogen, total phosphorus, sucrase, urease, acid phosphatase, catalase, and microbial biomass carbon, nitrogen, and phosphorus showed higher in 7-year-old stand than other two stands of CFP. The nonmetric multidimensional scaling analysis revealed that the soil microbial species composition was significantly different in three stand ages of CFP. The redundancy and canonical correspondence analysis indicated that the soil urease and microbial biomass nitrogen were the main factors affecting soil bacterial and fungal species composition. Our findings suggested that soil microbial diversity and community structure were inconsistent with changes in soil nutrients and enzyme activities during CFP development, and enhancing stand nurturing and soil nutrient accumulation in the mid-development stage were beneficial to the sustainable management of CFP.

Loss of ADP-glucose transporter in barley sex1 mutant caused shrunken endosperm but with elevated protein and ß-glucan content in whole meal.

Grain shape and plumpness affect barley yield. Despite numerous studies on shrunken endosperm mutants in barley, their molecular mechanism and application potential in the food industry are largely unknown. Here, map-based cloning, co-segregation analyses, and allelic variant validation revealed that the loss of HORVU6Hr1G037950 encoding an ADP-glucose transporter caused the shrunken endosperm in sex1. Haplotype analysis suggested that hap4 in the promoter sequence was positively related to the hundred-grain weight showing a breeding potential. A pair of near-isogenic lines targeting HORVU6Hr1G037950 was produced and characterized to investigate molecular mechanisms that SEX1 regulates endosperm development. Results presented that the absence of the SEX1 gene led to the decrease of starch content and A-type granules size, the increase of ß-glucan, protein, gelatinization temperature, soluble sugar content, amylopectin A chains, and B1 chains. Enzymatic activity, transcriptome and metabolome analyses revealed the loss of SEX1 results in an impaired ADP-glucose-to-starch conversion process, consequently leading to higher soluble sugar contents and lower starch accumulation, thereby inducing a shrunken-endosperm phenotype in sex1. Taken together, this study provides new insights into barley grain development, and the elevated protein and ß-glucan contents of the whole meal in sex1 imply its promising application in the food industry.

Characterization and application of Fe-modified biochar alleviating Cr(VI) stress in pak choi seedling cultivated in Cr-polluted hydroponics.

Chromium (Cr) is one of the common environmental pollutants, which causes severe health hazards on human health and environmental security. In this study, we characterized two biochars, a raw biochar (RBC) and a Fe-modified biochar (MBC) made from poplar wood chips and determined the effect of the two biochars on remediation of hexavalent chromium (Cr(VI)) in hydroponic system by monitoring Pak choi growth. Results showed the surface area, pore number and pore volume were significantly higher in MBC than in PBC, but the pore size was larger in PBC than in MBC. When compared to the control, low concentrations of Cr(VI) (≤2 mg L-1) promoted the growth and biomass production of Pak choi by 10-78%. In contrast, the high concentrations of Cr(VI) (≥4 mg L-1) showed a significantly reduction of the growth and biomass production of Pak choi by 10-28%. Fe-modified biochar (MBC) had a more significant impact than RBC on the remediation of Cr in the Cr(VI) pollution and improved growth and biomass production of Pak choi to a greater extent. Our study indicated that MBC has a better effect on degrading Cr(VI) pollution. The findings provide scientific basis and reference for the remediation of heavy metals in aquatic ecosystems by using biochar.

Biomass Production and Carbon Stocks in Poplar-Crop Agroforestry Chronosequence in Subtropical Central China.

Agroforest systems have been widely recognized as an integrated approach to sustainable land use for addressing the climate change problem because of their greater potential to sequester atmospheric CO2 with multiple economic and ecological benefits. However, the nature and extent of the effects of an age-sequence of agroforestry systems on carbon (C) storage remain largely unknown. To reveal the influence of different aged poplar-crop systems on C stocks, we investigated the variation in biomass and C storage under four aged poplar-crop agroforest systems (3-, 9-, 13-, and 17-year-old) in the Henan province of China. The results showed that stand biomass increased with forest age, ranging from 26.9 to 121.6 t/ha in the corresponding four aged poplar-crop systems. The poplar tree biomass accounted for >80% of the total stand biomass in these poplar-crop agroforestry systems, except in the 3-year-old agroforestry system. The average stand productivity peaked in a 9-year-old poplar-crop system (11.8 t/ha/yr), the next was in 13- and 17-year-old agroforestry systems, and the minimum was found in 3-year-old poplar-crop stands (4.8 t/ha/yr). The total C stocks increased, with aging poplar-crop systems ranging from 99.7 to 189.2 t/ha in the studied agroforestry systems. The proportion of C stocks accounted for about 6, 25, and 69% of the total C stocks in the crop, poplar tree, and soil components in all studied agroforestry ecosystems, respectively. Our results suggested that the poplar-crop system, especially in productive and mature stages, is quite an effective agroforestry model to increase the study site's biomass production and C stocks. This study highlighted the importance of agroforestry systems in C storage. It recommended the poplar-crop agroforest ecosystems as a viable option for sustainable production and C mitigation in the central region of China.

Ecological Stoichiometry and Stock Distribution of C, N, and P in Three Forest Types in a Karst Region of China.

Ecological stoichiometry plays important roles in understanding the nutrient constraints on tree growth and development, as well in maintaining ecosystem services in forests, yet the characteristics of carbon:nitrogen:phosphorous (C:N:P) stoichiometry in forests under karst environment have not been sufficiently evaluated. In this study, concentration, distribution, stocks of Nitrogen (N) and Phosphorous (P), and ecological stoichiometry were studied in three common forest types: Masson pine natural forests (MPNF), Masson pine plantation forests (MPPF), and Slash pine plantation forests (SPPF) in a karst region of southwestern China. Results showed that N concentrations were higher in overstory than in understory and litter in the studied forests. However, P concentration was relatively low in overstory component of the forested ecosystems. Meanwhile, the N and P concentrations were higher in SPPF in the stem and litter, while these contents were higher in MPPF and MPNP in the overstory and understory. The N and P stocks ranged from 5.7-6.2 t ha-1, and 0.5-0.6 t ha-1 in the examined forests. The ecological stoichiometry of C:N:P in the three forest types was similar in litter (46-49:2:1), and relatively steady in soil (250-320:13-16:1) and tree leaf (100-200:14-20:1). Soil P status was the primary limiting factor in affecting tree growth in MPPF and SPPF (N:P ratio > 16), while both N and P conditions were the main restrictive factors in MPNP (N:P ratio = 15) in the study area. Our study provides scientific references and useful datasets of C:N:P stoichiometry for sustainable management of forest ecosystems in karst regions.

Identification and validation of two major QTLs for spikelet number per spike in wheat (Triticum aestivum L.).

The total number of spikelets (TSPN) and the number of fertile spikelets (FSPN) affect the final number of grains per spikelet in wheat. This study constructed a high-density genetic map using 55K single nucleotide polymorphism (SNP) arrays from a population of 152 recombinant inbred lines (RIL) from crossing the wheat accessions 10-A and B39. Twenty-four quantitative trait loci (QTLs) for TSPN and 18 QTLs for FSPN were localized based on the phenotype in 10 environments in 2019-2021. Two major QTLs, QTSPN/QFSPN.sicau-2D.4 (34.43-47.43 Mb) and QTSPN/QFSPN.sicau-2D.5(32.97-34.43 Mb), explained 13.97%-45.90% of phenotypic variation. Linked kompetitive allele-specific PCR (KASP) markers further validated these two QTLs and revealed that QTSPN.sicau-2D.4 had less effect on TSPN than QTSPN.sicau-2D.5 in 10-A×BE89 (134 RILs) and 10-A×Chuannong 16 (192 RILs) populations, and one population of Sichuan wheat (233 accessions). The alleles combination haplotype 3 with the allele from 10-A of QTSPN/QFSPN.sicau-2D.5 and the allele from B39 of QTSPN.sicau-2D.4 resulted in the highest number of spikelets. In contrast, the allele from B39 for both loci resulted in the lowest number of spikelets. Using bulk-segregant analysis-exon capture sequencing, six SNP hot spots that included 31 candidate genes were identified in the two QTLs. We identified Ppd-D1a from B39 and Ppd-D1d from 10-A and further analyzed Ppd-D1 variation in wheat. These results identified loci and molecular markers with potential utility for wheat breeding and laid a foundation for further fine mapping and cloning of the two loci.

Pangenomic analysis identifies structural variation associated with heat tolerance in pearl millet.

Pearl millet is an important cereal crop worldwide and shows superior heat tolerance. Here, we developed a graph-based pan-genome by assembling ten chromosomal genomes with one existing assembly adapted to different climates worldwide and captured 424,085 genomic structural variations (SVs). Comparative genomics and transcriptomics analyses revealed the expansion of the RWP-RK transcription factor family and the involvement of endoplasmic reticulum (ER)-related genes in heat tolerance. The overexpression of one RWP-RK gene led to enhanced plant heat tolerance and transactivated ER-related genes quickly, supporting the important roles of RWP-RK transcription factors and ER system in heat tolerance. Furthermore, we found that some SVs affected the gene expression associated with heat tolerance and SVs surrounding ER-related genes shaped adaptation to heat tolerance during domestication in the population. Our study provides a comprehensive genomic resource revealing insights into heat tolerance and laying a foundation for generating more robust crops under the changing climate.

Genome-Wide Association Mapping of QTL Underlying Groat Protein Content of a Diverse Panel of Oat Accessions.

Groat protein content (GPC) is a key quality trait attribute in oat. Understanding the variation of GPC in oat germplasms and identifying genomic regions associated with GPC are essential for improving this trait. In this study, the GPC of 174 diverse oat accessions was evaluated in three field trials. The results showed a wide variation in GPC, ranging from 6.97% to 22.24% in this panel. Hulless oats displayed a significantly higher GPC compared to hulled oats across all environments. A GWAS analysis was performed based on 38,313 high-quality SNPs, which detected 27 non-redundant QTLs with 41 SNPs significantly associated with GPC. Two QTLs on chromosome 6C (QTL16) and 4D (QTL11) were consistently detected in multiple environments, with QTL16 being the most significant and explaining the highest proportion of the phenotypical variation in all tested environments except in CZ20. Haplotype analysis showed that the favorable haplotypes for GPC are more prevalent in hulless oats. These findings provide a foundation for future efforts to incorporate favorable alleles into new cultivars through introgression, fine mapping, and cloning of promising QTLs.

Effects of Exponential N Application on Soil Exchangeable Base Cations and the Growth and Nutrient Contents of Clonal Chinese Fir Seedlings.

Nitrogen (N) is an essential macronutrient for plant function and growth and a key component of amino acids, which form the building blocks of plant proteins and enzymes. However, misuse and overuse of N can have many negative impacts on the ecosystem, such as reducing soil exchangeable base cations (BCs) and causing soil acidification. In this research, we evaluated clonal Chinese fir (Cunninghamia lanceolata (Lamb.) Hook) seedlings grown with exponentially increasing N fertilization (0, 0.5, 1, 2 g N seedling-1) for a 100-day trial in a greenhouse. The growth of seedlings, their nutrient contents, and soil exchangeable cations were measured. We found that N addition significantly increased plant growth and N content but decreased phosphorous (P) and potassium (K) contents in plant seedlings. The high nitrogen (2 g N seedling-1) treated seedlings showed a negative effect on growth, indicating that excessive nitrogen application caused damage to the seedlings. Soil pH, soil exchangeable base cations (BCs), soil total exchangeable bases (TEB), soil cation exchange capacity (CEC), and soil base saturation (BS) significantly decreased following N application. Our results implied that exponential fertilization resulted in soil acidification and degradation of soil capacity for supplying nutrient cations to the soil solution for plant uptake. In addition, the analysis of plants and BCs revealed that Na+ is an important base cation for BCs and for plant growth in nitrogen-induced acidified soils. Our results provide scientific insights for nitrogen application in seedling cultivation in soils and for further studies on the relationship between BCs and plant growth to result in high-quality seedlings while minimizing fertilizer input and mitigating potential soil pollution.

Novel Weighting Method for Evaluating Forest Soil Fertility Index: A Structural Equation Model.

Understanding nutrient quantity and quality in forest soils is important for sustainable management of forest resources and maintaining forest ecosystem services. In this study, six soil nutrient indicators, including soil organic matter (SOM), total nitrogen (TN), total phosphorus (TP), available nitrogen (AN), available phosphorus (AP), and available potassium (AK) were measured in five different aged stands of Chinese fir forests in subtropical China. A structural equation model (SEM) was developed based on these soil nutrients indicators in order to better evaluate the soil fertility index (SFI) in these studied forests. The results show that soil nutrient contents changed with the soil depth in different age groups. The SOM decreased in a specific order: over mature > mature > near mature > middle > young stands. The TN content of the soil gradually decreased with increased soil depth throughout all age groups. The SEM indicated that the TN had the highest weight of 0.4154, while the TP had the lowest weight at 0.1991 for estimating the SFI. The weights of other indicators (AN, SOM, AP, and AK) ranged 0.2138−0.3855 in our study. The established SEM satisfied the fitness reference values and was able to accurately describe the forest soil nutrient status through the SFI. The overall SFI values were significantly higher in over mature stands than in young-aged stands and in topsoil than in deeper soil in all examined forests. Soil TN, AP, and AK were the most important nutrient indicators to the evaluation of the SFI in the study sites. The results confirmed that the SEM was suitable to estimate the weights of the SFI and better describe the soil nutrient status in forests. Our research provides an innovative approach to assess a soil nutrient status and soil fertility and provides a scientific basis for accurate implementation of soil nutrient assessment in forest ecosystems.

Effects of perfluorinated compounds homologues on chemical property, microbial composition, richness and diversity of urban forest soil.

Perfluorinated compounds (PFCs), as an important class of new persistent organic pollutants, are widely distributed in the environment. Yet the effects of different types and concentrations of PFCs on soil microbial community in urban forest ecosystems are remain uncertain. Here, two typical PFCs, perfluorooctanoic acid (PFOA) and perfluorooctane sulfonic acid (PFOS), were selected to carry out a pot experiment in greenhouse with singly and joint treatment at different concentrations, to examine their effects on composition and diversity of soil microorganisms and availability of soil macronutrients by using high-throughput Illumina sequencing approach. The results showed both PFOA and PFOS application significantly increased soil NO3--N and NH4+-N content, but did not alter total phosphorus content, compared to the control check (CK) treatments. Total potassium content was reduced in PFOA treatments but increased in PFOS and PFOA×PFOS treatments. The most dominant bacterial phylum was Chloroflexi in low and medium PFCs concentrations and the CK treatments, but it was switched to Acidobacteria in high concentrations. No obvious change was detected for the composition of the dominant fungi community in PFCs treatments compared to the CK treatments. With the increase of PFCs concentrations, soil bacterial richness decreased but its diversity increased, whereas the richness and diversity of fungal community usually decreased. Redundancy analyses revealed that soil fungal community was more sensitive to PFCs pollutants than soil bacterial communities. Further data analysis revealed by structural equation model (SEM) that the PFCs exposed for 60 days indirectly affects the diversity and richness of soil bacteria and fungi by directly affecting NO3--N and NH4+-N content. The results suggested the concentration of PFCs pollutants played a primary role in determining the composition, richness and diversity of forest soil microbial communities.

Identification and validation of a locus for wheat maximum root length independent of parental reproductive environment.

Maximum root length (MRL) plays an important role in the uptake of nutrients and resisting abiotic stresses. Understanding the genetic mechanism of root development is of great significance for genetic improvement of wheat. Previous studies have confirmed that parental reproductive environment (PRE) has a significant impact on growth and development of the next generation in the whole life cycle of a given plant. In this study, a recombinant inbred line population genotyped using the Wheat55K SNP array, was used to map quantitative trait loci (QTL) for wheat seedling MRL based on the harvested seeds from five different PREs. A total of 5 QTL located on chromosomes 3D and 7A were identified. Among them, QMrl.sicau-2SY-3D.2 located in a 4.0 cM interval on chromosome 3D was likely independent of PREs. QMrl.sicau-2SY-7A.2 was detected in two tests and probably influenced by PREs. The effect of QMrl.sicau-2SY-3D.2 was further validated using the tightly linked kompetitive allele specific PCR (KASP) marker, KASP-AX-111589572, in populations with different genetic backgrounds. Lines with a combination of positive alleles from QMrl.sicau-2SY-3D.2 and QMrl.sicau-2SY-7A.2 have significantly longer MRL. Furthermore, four genes (TraesCS3D03G0612000, TraesCS3D03G0608400, TraesCS3D03G0613600, and TraesCS3D03G0602400) mainly expressed in wheat root were predicted to be associated with root growth. Taken together, this study reports on a major QTL independent of PREs and lays a foundation for understanding the regulation mechanism of wheat MRL at the seedling stage.

Soil Nitrogen Transformation Process Influenced by Litterfall Manipulation in Two Subtropical Forest Types.

Nitrogen (N) is often recognized as the primary limiting nutrient element for the growth and production of forests worldwide. Litterfall represents a significant pathway for returning nutrients from aboveground parts of trees to the soils and plays an essential role in N availability in different forest ecosystems. This study explores the N transformation processes under litterfall manipulation treatments in a Masson pine pure forest (MPPF), and Masson pine and Camphor tree mixed forest (MCMF) stands in subtropical southern China. The litterfall manipulation included litterfall addition (LA), litterfall removal (LR), and litterfall control (LC) treatments. The project aimed to examine how litterfall inputs affect the soil N process in different forest types in the study region. Results showed that soil ammonium N (NH4 +-N) and nitrate N (NO3 --N) content increased under LA treatment and decreased under LR treatment compared to LC treatment. LA treatment significantly increased soil total inorganic N (TIN) content by 41.86 and 22.19% in MPPF and MCMF, respectively. In contrast, LR treatment decreased the TIN content by 10 and 24% in MPPF and MCMF compared to LC treatment. Overall, the soil net ammonification, nitrification, and N mineralization rates were higher in MCMF than in MPPF; however, values in both forests were not significantly different. LA treatment significantly increased annual net ammonification, nitrification, and mineralization in both forest types (p < 0.05) compared to LC treatment. LR treatment significantly decreased the values (p < 0.05), except for ammonification, where LR treatment did not differ substantially compared to LC treatment. Our results suggested that changes in litterfall inputs would significantly alter soil N dynamics in studied forests of sub-tropical region. Moreover, mixed forest stands have higher nutrient returns due to mixed litter and higher decomposition compared to pure forest stands.

Reference genome assemblies reveal the origin and evolution of allohexaploid oat.

Common oat (Avena sativa) is an important cereal crop serving as a valuable source of forage and human food. Although reference genomes of many important crops have been generated, such work in oat has lagged behind, primarily owing to its large, repeat-rich polyploid genome. Here, using Oxford Nanopore ultralong sequencing and Hi-C technologies, we have generated a reference-quality genome assembly of hulless common oat, comprising 21 pseudomolecules with a total length of 10.76 Gb and contig N50 of 75.27 Mb. We also produced genome assemblies for diploid and tetraploid Avena ancestors, which enabled the identification of oat subgenomes and provided insights into oat chromosomal evolution. The origin of hexaploid oat is inferred from whole-genome sequencing, chloroplast genomes and transcriptome assemblies of different Avena species. These findings and the high-quality reference genomes presented here will facilitate the full use of crop genetic resources to accelerate oat improvement.

Polyploidization affects the allelic variation of jasmonate-regulated protein Ta-JA1 belonging to the monocot chimeric jacalin (MCJ) family in wild emmer wheat.

The jasmonate-regulated protein Ta-JA1 belongs to the monocot chimeric jacalin (MCJ) family and plays a vital role in stress resistance in wheat. However, the impact of wheat polyploidization on Ta-JA1 remains unclear. In this study, 149 members of the MCJ family were identified among members of Triticeae using a genome-wide approach. The genes were resolved into three clades; MCJ genes in each clade were derived from different donor genes during evolution. Segmental duplication may have been the primary driver, compared with tandem duplication, of expansion in the MCJ family of wheat. Gene loss and acquisition occurred during tetraploidization, and the core expansion of the family occurred after tetraploidization. Sequencing data for 2104 accessions of T. aestivum and 99 accessions of T. dicoccoides showed that Ta-JA1-2A and Ta-JA1 were highly conserved in common wheat, and four alleles (TdJA1-Ax2, TdJA1-Ay2, TdJA1-Ax3, and TdJA1-Ay3) were detected in T. dicoccoides. Using gene-specific markers, one AsJA1-B allele was detected in 11 Ae. speltoides accessions and one TuJA1-Ax1 allele was detected in 70 T. urartu accessions. Six alleles were detected on chromosome 2A: TdJA1-Ax1 (13 accessions), TdJA1-Ay1 (57 accessions), TdJA1-Ax2 (23 accessions), TdJA1-Ay2 (42 accessions), TdJA1-Ax3 (29 accessions), and TdJA1-Ay3 (251 accessions). Only one allele (TdJA1-B) on chromosome 2B was detected in 415 T. dicoccoides accessions. A geographical distribution analysis revealed that Israel hosted higher allelic variation than other regions. Quantitative reverse transcription PCR analysis indicated that divergence in expression has occurred among Ta-JA1 alleles and, notably, TdJA1-Ax1 and TdJA1-Ay1 showed significantly higher expression levels than the other four allelic types in T. dicoccoides. The present results contribute to an improved understanding of the effects of polyploidization on the MCJ gene family and the functions of Ta-JA1, and may be useful to enrich common wheat germplasm resources.

Position Validation of the Dwarfing Gene Dw6 in Oat (Avena sativa L.) and Its Correlated Effects on Agronomic Traits.

An F6 : 8 recombinant inbred line (RIL) population derived from the cross between WAOAT2132 (Dw6) and Caracas along with the two parents were used to evaluate the genetic effects of Dw6 dwarfing gene on plant height and other agronomic traits in oat (Avena sativa L.) across three environments, and develop closely linked markers for marker-assisted selection (MAS) for Dw6. The two parents differed in all investigated agronomic traits except for the number of whorls. The RIL lines showed a bimodal distribution for plant height in all three tested environments, supporting the height of this population was controlled by a single gene. Dw6 significantly reduced plant height (37.66∼44.29%) and panicle length (13.99∼22.10%) but without compromising the coleoptile length which was often positively associated with the reduced stature caused by dwarfing genes. Dw6 has also strong negative effects on hundred kernel weight (14.00∼29.55%), and kernel length (4.21∼9.47%), whereas the effects of Dw6 on the kernel width were not uniform across three environments. By contrast, lines with Dw6 produced more productive tillers (10.11∼10.53%) than lines without Dw6. All these together suggested the potential yield penalty associated with Dw6 might be partially due to the decrease of kernel weight which is attributed largely to the reduction of kernel length. Eighty-one simple sequence repeat (SSR) primer pairs from chromosome 6D were tested, five of them were polymorphic in two parents and in two contrasting bulks, confirming the 6D location of Dw6. By using the five polymorphic markers, Dw6 was mapped to an interval of 1.0 cM flanked by markers SSR83 and SSR120. Caution should be applied in using this information since maker order conflicts were observed. The close linkages of these two markers to Dw6 were further validated in a range of oat lines. The newly developed markers will provide a solid basis for future efforts both in the identification of Dw6 in oat germplasm and in the determination of the nature of the gene through positional cloning.

New evidence confirming the CD genomic constitutions of the tetraploid Avena species in the section Pachycarpa Baum.

The tetraploid Avena species in the section Pachycarpa Baum, including A. insularis, A. maroccana, and A. murphyi, are thought to be involved in the evolution of hexaploid oats; however, their genome designations are still being debated. Repetitive DNA sequences play an important role in genome structuring and evolution, so understanding the chromosomal organization and distribution of these sequences in Avena species could provide valuable information concerning genome evolution in this genus. In this study, the chromosomal organizations and distributions of six repetitive DNA sequences (including three SSR motifs (TTC, AAC, CAG), one 5S rRNA gene fragment, and two oat A and C genome specific repeats) were investigated using non-denaturing fluorescence in situ hybridization (ND-FISH) in the three tetraploid species mentioned above and in two hexaploid oat species. Preferential distribution of the SSRs in centromeric regions was seen in the A and D genomes, whereas few signals were detected in the C genomes. Some intergenomic translocations were observed in the tetraploids; such translocations were also detected between the C and D genomes in the hexaploids. These results provide robust evidence for the presence of the D genome in all three tetraploids, strongly suggesting that the genomic constitution of these species is DC and not AC, as had been thought previously.

Spike Density Quantitative Trait Loci Detection and Analysis in Tetraploid and Hexaploid Wheat Recombinant Inbred Line Populations.

Spike density (SD) is an agronomically important character in wheat. In addition, an optimized spike structure is a key basis for high yields. Identification of quantitative trait loci (QTL) for SD has provided a genetic basis for constructing ideal spike morphologies in wheat. In this study, two recombinant inbred line (RIL) populations (tetraploid RIL AM and hexaploid RIL 20828/SY95-71 (2SY)) previously genotyped using the wheat55K SNP array were used to identify SD QTL. A total of 18 QTL were detected, and three were major and one was stably expressed (QSd.sau-2SY-7A.2, QSd.sau-AM-5A.2, QSd.sau-AM-7B, and QSd.sau-2SY-2D). They can explain up to 23.14, 19.97, 12.00, and 9.44% of phenotypic variation, respectively. QTL × environment and epistatic interactions for SD were further analyzed. In addition, pyramiding analysis further revealed that there were additive effects between QSd.sau-2SY-2D and QSd.sau-2SY-7A.2 in 2SY, and QSd.sau-AM-5A.2 and QSd.sau-AM-7B in AM. Pearson's correlation between SD and other agronomic traits, and effects of major or stable QTL on yield related traits indicated SD significantly impacted spike length (SL), spikelet number per spike (SNS) and kernel length (KL). Several genes related to spike development within the physical intervals of major or stable QTL were predicted and discussed. Collectively, our research identified QTL with potential applications for modern wheat breeding and broadening the genetic basis of SD.