Sinapis arvensis, belonging to the genus Sinapis of the family Brassicaceae, has good agronomic characters that make it a valuable genetic resource for crop improvement and is a cytoplasmic source of heterologous cytoplasmic male sterility (CMS). In addition, S. arvensis has played an important role in the evolution of the six major cultivated Brassica species involved in the triangle of U. Using next-generation sequencing, we assembled and revealed the gene composition of S. arvensis cytoplasmic genome. The chloroplast genome comprises 153,590 bp, with 112 individual genes, including 4 rRNA, 29 tRNA, and 79 protein-coding genes. The mitochondrial genome comprises 240,024 bp, with 54 genes, including 18 tRNA, three rRNA and 33 protein-coding genes. Genome structure and evolutionary analysis indicated that the sequences of the S. arvensis organellar genomes were more similar to those of Brassica nigra and B. carinata than to those of other Brassicaceae species. Four mitochondrial open reading frames displaying chimeric structural features and encoding hypothetical proteins with transmembrane domains may account for the infertility of Nsa CMS previously derived from somatic cell hybridization between B. napus and S. arvensis. These results will not only contribute to utilize the germplasm resource of S. arvensis, and comprehend the evolution of organelle genomes within the Brassicaceae family, but also help to identify genes conditioning the alloplasmic male sterility of Nsa CMS in B. napus.

Pre-harvest sprouting (PHS) influences yield and end-use quality of bread wheat. Developing varieties with PHS resistance is the most effective way to reduce this problem. In this study, a panel of 725 Chinese wheat accessions were evaluated for PHS resistance in three environments. There was abundant variation in PHS resistance and 63 accessions showing high resistance had germination rates of less than 10% across three experiments. The distribution of three causal single nucleotide polymorphisms in TaPHS1 at bases −222, +646, and +666 were assessed and frequencies were determined. Favorable alleles conferring PHS resistance were identified for each locus. Haplotype analysis showed that bases C, G, and A at each of the three loci comprised the best haplotype for PHS resistance, whereas TAT showed the highest sprouting rate. Accessions with the superior TaPHS1 haplotypes proved to be resistant to PHS providing a basis to develop varieties with PHS resistance through marker assisted breeding.

Cotton fibers are single cells originating in the epidermis of cotton ovules, and serve as the largest natural fiber source for the textile industry. In theory, all epidermal cells have the potential to develop into fibers, but only 15%-25% of epidermis cells develop into commercially viable lint fibers. We previously showed that GhLac1 participates in cotton defense against biotic stress. Here we report that GhLac1 also has a role in cotton fiber development. GhLac1 RNAi lines in cotton showed increased differentiation of fiber initials from epidermis and shortened fiber length, resulting in unchanged lint percentage. Suppression of GhLac1 expression led to constitutively hyperaccumulated jasmonic acid (JA) and flavonoids in ovules and fiber cells. In vitro ovule culture experiments confirmed the distinct roles of JA and flavonoids in fiber initiation and elongation, and showed that fiber development is spatially regulated by these chemicals: the increased fiber initiation in GhLac1 RNAi lines is caused by hyperaccumulated JA and rutin content during the fiber initiation stage and shortened fiber length is caused by constitutively increased JA and naringenin content during the fiber elongation stage.

Phosphorus use efficiency (PUE) can be improved through cultivation techniques and breeding. However, little is known about rice (Oryza sativa L.) agronomic and physiological traits associated with high PUE. We characterized the agronomic and physiological traits of rice varieties with different tolerances to low phosphorus in nutrient solution. Two varieties with strong tolerance to low phosphorus (STVs) and two with weak tolerance (WTVs) were grown at normal (NP, control) and low phosphorus (LP, 1/20 of NP) concentrations. Plants grown at LP produced significantly lower grain yield than those grown at NP. WTVs yields were lower than STVs yields. Compared to NP, LP significantly increased phosphorus translocation efficiency (PTE), internal phosphorus efficiency (IPE) and phosphorus harvest index (PHI). Under the LP condition, PTE and IPE were higher for STVs than for WTVs. LP also reduced tiller number, shoot biomass, leaf area index (LAI), leaf photosynthetic rate, and mean root diameter of both kinds of varieties at the main growth stages, but to a lower extent in STVs. LP significantly increased the number of productive tillers, root biomass, root-shoot ratio, root bleeding rate, and root acid phosphatase (RAP) activity. Total root length, root oxidation activity (ROA), and root total and active absorbing surface areas for STVs were significantly increased under LP, whereas the opposite responses were observed for WTVs. Total root length, ROA, root bleeding rate, root active absorbing surface area, and RAP activity were positively and significantly correlated with grain yield, PTE, and IPE. These results suggest that the tolerance of rice varieties to a low-phosphorus growth condition is closely associated with root growth with higher biomass and activity.

In rainfed areas of northwestern China, maize production is constrained mainly by low temperature during early growth and water limitation during the entire growth period. Plastic film mulching is commonly used to increase maize yield in this area, because it increases topsoil temperature and moisture content as well as water use efficiency. However, the physiological and anatomical bases of maize yield improvement with plastic film mulching are not well understood. The effects of plastic film mulching and planting density on maize yield, photosynthetic characteristics, respiration, leaf anatomy, and root growth were studied in a two-year field experiment conducted on the Loess Plateau of China in 2017 and 2018. The experiment used a split-split plot design with two mulching treatments (plastic film mulching and no mulching), two planting densities (7.5×10⁴ and 10.5×10⁴ plants ha⁻¹), and two maize cultivars, Zhengdan 958 and Xianyu 335. Compared with no mulching, plastic film mulching increased maize yields by 31.1%-46.4% in 2017 and 3.6%-34.7% in 2018. Compared with low planting density, high planting density significantly increased and slightly reduced yields of both cultivars in the dry year 2017 and the rainy year 2018, respectively. Plastic film mulching increased photosynthesis and respiration as well as leaf stomatal density and aperture. Photosynthetic rate, dark respiration, and stomatal conductance and aperture were lower at high planting than at low planting density. Maize yield was positively correlated with photosynthesis, dark respiration, and stomatal aperture. Mulching increased root dry weight and length in the 0-20 cm soil layer and root activity at maturity. Overall, the changes in root growth and leaf anatomy resulted in increased photosynthesis and dark respiration, and the increased photosynthesis contributed to the increase in grain yield and biomass production under plastic film mulching conditions. Our results increase understanding of the physiological mechanisms by which plastic film mulching increases maize yield in water- and temperature-limited areas.

Wheat (Triticum aestivum) is necessary for global food security. The necrotrophic fungus Rhizoctonia cerealis is the causal agent of sharp eyespot, a devastating disease of wheat. Although the Elongator complex, composed of six subunits, has been implicated in growth, development, and innate immunity in Arabidopsis, little is known about its functions in wheat or the involvement of Elongator subunit 4 in histone acetylation. In this study, we identified the Elongator subunit 4-encoding gene TaELP4 in wheat resistance response to R. cerealis, and verified that TaELP4 increased histone acetylation in regions of defense-associated genes and regulated immune response to R. cerealis. TaELP4 was more highly expressed in resistant than in susceptible wheat cultivars and was induced in resistant wheat after infection by R. cerealis. Silencing of TaELP4 in wheat not only impaired resistance to R. cerealis, but also repressed both histone acetylation levels and the expression of a subset of defense-associated genes, including TaAGC1, TaCPK7-D, TaPAL5, Defensin, and Chitinase2. Ectopic expression of TaELP4 in Arabidopsis increased histone acetylation levels in coding and promoter regions of defense genes and increased their transcription, leading to increased resistance to infection by the pathogen Botrytis cinerea. These results suggest that TaELP4 positively regulates innate immune responses of wheat and Arabidopsis to R. cerealis and B. cinerea by increasing histone acetylation levels of defense-associated genes and increasing their transcription. This study has shed light on the involvement of TaELP4 in histone acetylation and resistance response against R. cerealis. TaELP4 may potentially be used to improve wheat resistance against sharp eyespot.

Structural variation is a major type of genetic variation that can potentially induce powerful genetic effects. In this study, we examined the Inv(A07)p1.09p2.23 genetic inversion in brown fibre cotton at the individual and population genetics levels. A dark-brown fibre mutant that resulted from a distant hybridization between Gossypium barbadense and G. hirsutum, and a natural population including 30 dark-brown, 70 light-brown and 21 white fibre cotton accessions were collected to perform a functional study of this micro-inversion. The results showed that Inv(A07)p1.09p2.23 can be detected by high-throughput resequencing method, and induce micro-deletion, gene disruption (Ghir_A07G000980) and abnormal gene expression in the breakpoint regions. Inv(A07)p1.09p2.23 existed in only dark-brown fibre cotton, had undergone negative selection in elite brown fibre cultivars, and was significantly associated with fibre colour and nine fibre traits. In the Inv(A07)p1.09p2.23 region, nucleotide diversity was lower, recombination was absent, and linkage disequilibrium was higher. Overall, this inversion event in dark-brown fibre cotton produced significant genetic effects, and this study will guide us to better understand the genetic effects of inversion events in dark-brown fibre cotton.

Alternate wetting and drying (AWD) irrigation has been widely used as an efficient rice production method to obtain better yield without continuous flooding (CF) of the paddy field. However, how this practice affects gene expression to regulate rice physiology and morphology is largely unknown. In this study, we used two rice varieties, Nipponbare, a lowland rice cultivar, and Gaoshan 1, an upland cultivar, and found that root dry weight (RDW) and root oxidation activity (ROA) in both cultivars substantially increased in response to AWD. We then analyzed the differences in transcriptome profiles of their roots irrigated in AWD vs. CF conditions. AWD responsive genes are mainly involved in lignin biosynthetic pathway and phytohormone signal transduction pathway and belong mainly to bHLH, bZIP, NAC, WRKY, and HSF transcription factor families. We discussed how these differentially expressed genes may contribute to the morphological adaptations observed in roots exposed to AWD. This analysis also provides useful information to explain the similarities and differences in adaptation to AWD irrigation between the two rice ecotypes.

microRNA 160 (miR160), targeting auxin response factors (ARFs), plays many roles in plant development. We investigated the role of the miR160/ARF axis in regulation of cotton seed size. Suppressing miR160 activity, specifically in the seed coat, led to smaller seeds and less fiber production owing to attenuated growth of the maternal integument. Scanning electron microscopy and histology showed that expansion of cells in the integument was retarded in miR160-suppressed lines. Four GhARF genes were targeted by miR160 and were upregulated in miR160-suppressed lines, indicating that a miR160/ARF axis is present in cotton. Five genes (Ghir_A05G003740, Scaffold1878G000010, Ghir_D09G024980, Ghir_A11G010730, and Ghir_A05G041590), associated with reduced seed development were downregulated in miR160-suppressed lines. Our results suggest that the miR160/ARF axis controls maternal integument growth to influence seed size by directly or indirectly regulating seed development-associated genes.

Awns play an important role in seed dispersal and photosynthesis of spikes. Three major awn inhibitors (Hd, B1, and B2) are reported in wheat. However, the molecular mechanism underlying awnlessness remained unknown until recently. In this study, we identified two F₈ recombinant inbred lines (RILs) that were segregating for awn length. In order to identify the causal gene for awn length in the heterozygous inbred families (HIFs), SNPs were called from RNA sequencing (RNA-Seq) data for HIF-derived progenies with long and short awns. SNPs between long and short awn plants were evenly distributed on chromosomes (chr) other than chromosome 5A. SNPs on chr 5A were clustered in a region distal 688 Mb on the long arm, where inhibitor B1 was located. This suggested that B1 was the causal segregating locus. We precisely mapped B1 to ~1 Mb region using two HIF-derived families. Considering that the lines segregated for long, intermediate and short awn phenotypes we speculated that B1 should have a dosage effect on awn length. Two differentially expressed genes (DEGs) located in the candidate region were regarded as candidate genes for B1, because the molecular expression pattern was consistent with the phenotype. HIFs with long and short awns showed no difference on grain yield and other agronomic traits.

This study evaluates the changes caused by breeding in the genotype by environment (G × E) interaction of the durum wheat varieties most widely cultivated in Spain after the Green Revolution. A set of 12 cultivars was tested in 27 environments, which are understood as the combination of different sites, years, and treatments (water regime and planting dates), representative of the durum wheat growing conditions in Spain with average grain yields (GY) ranging between 2.8 and 9.1 Mg ha⁻¹. The most important environmental factors affecting the G × E interaction for yield were themaximum and the mean temperature during the entire crop cycle. An improvement in genetic yield was observed in warm environments and under optimal water conditions that resemble those where the germplasm originated (essentially as advanced lines) before its release in Spain. Therefore, the adaptation of semi-dwarf durum in Spain has shown a tendency to specific adaptation rather than large-scale adaptation. Two different patterns of selection have been reported due the G × E interaction and changes in the ranking of genotypes: in the high yielding environments (GY > 5 Mg ha⁻¹), plants favor increased water uptake, with higher levels of transpiration and more open stomata (more negative values of carbon isotope composition, δ¹³C, and higher canopy temperature depression, CTD), whereas, in low yielding environments (GY < 5 Mg ha⁻¹) plants close their stomata and favor greater water use efficiency (less negative δ¹³C values and lower CTD values).

The stability of soybean (Glycine max L. Merrill) oil is determined mainly by its fatty acid (FA) composition. We evaluated the FA composition of 1025 Chinese soybean accessions collected from diverse ecoregions and grown in multiple locations and years. We observed highly significant differences (P<0.001) between accessions in palmitic acid (PA), stearic acid (SA), oleic acid (OA), linoleic acid (LA), and linolenic acid (LNA) contents. Growth year affected (P<0.001) the abundance of all FAs except PA. The mean PA, SA, OA, LA, and LNA contents were 12.2%, 3.8%, 21.5%, 54.2%, and 8.3%, respectively. The geographical origin of the accession influenced seed FA composition, indicating that accessions originating in each ecoregion tend to have distinct FA composition. We observed significant positive correlations among the three locations and between the two years, suggesting the high heritability and stability of individual accessions across contrasting environments. We also observed a relatively high negative correlation between the contents of OA and both LA and LNA (r=−0.90 and −0.59, respectively, each significant at P<0.001), providing a potential entry point for developing strains producing oil with higher OA and lower LA and LNA levels. These would be appropriate for specialized use in the food industry. Our results will be useful in breeding soybean with improved quality to meet human nutritional and industrial needs.

Crown root traits, including crown root angle (CRA), diameter (CRD), and number (CRN), are major determining factors of root system architecture, which influences crop production. In maize, the genetic mechanisms determining crown root traits in the field are largely unknown. CRA, CRD, and CRN were evaluated in a recombinant inbred line population in three field trials. High phenotypic variation was observed for crown root traits, and all measured traits showed significant genotype-environment interactions. Single-environment (SEA) and multi-environment (MEA) quantitative trait locus (QTL) analyses were conducted for CRA, CRD, and CRN. Of 46 QTL detected by SEA, most explained less than 10% of the phenotypic variation, indicating that a large number of minor-effect QTL contributed to the genetic component of these traits. MEA detected 25 QTL associated with CRA, CRD, and CRN, and 2 and 1 QTL were identified with significant QTL-by-environment interaction effects for CRA and CRD, respectively. A total of 26.1% (12/46) of the QTL identified by SEA were also detected by MEA, with many being detected in more than one environment. These findings contribute to our understanding of the phenotypic and genotypic patterns of crown root traits in different environments. The identified environment-specific QTL and stable QTL may be used to improve root traits in maize breeding.

Stripe or yellow rust (YR) and leaf rust (LR) cause large losses in wheat production worldwide. Resistant cultivars curtail the levels of losses. The present study aimed to identify quantitative trait loci (QTL) for YR and LR resistance in 147 F_2:6 recombinant inbred lines (RIL) derived from the cross Fuyu 3/Zhengzhou 5389. The RIL population and parents were genotyped with the Wheat55K single nucleotide polymorphism (SNP) array and simple sequence repeat (SSR) markers. All materials were also phenotyped for YR severity at Mianyang in Sichuan province and Baoding in Hebei province in the 2015/2016, 2016/2017, and 2017/2018 cropping seasons, and LR severity at Zhoukou in Henan province and at Baoding in 2017/2018. Eleven QTL for YR resistance and five for LR resistance were detected using inclusive composite interval mapping (IciMapping). Four of these QTL on chromosomes 1BL, 2BS, 3AL, and 5AL conferred resistance to both YR and LR. The QTL on 1BL was Lr46/Yr29, and that on 7BL might be Lr68. The QTL on chromosome 2BS was detected at a similar position to previously detected loci. QYr.hebau-3AL/QLr.hebau-3AL, QYr.hebau-5AL/QLr.hebau-5AL, QYr.hebau-7DL, QYr.hebau-4BS, QYr.hebau-6DL, and QYr.hebau-2AS are likely to be new. An SSR marker for QYr.hebau-7DL was developed and validated in a diverse wheat panel from China, suggesting effectiveness in different genetic backgrounds. These QTL with closely linked SNP and SSR markers could be useful for marker-assisted selection in wheat breeding programs targeting durable resistance to both diseases.

Carfentrazone-ethyl and tribenuron-methyl, the two widely used herbicides for weed control in field crops, frequently cause phytotoxicity to wheat seedlings in the field. In this study, a total of 697 wheat accessions containing three panels were scanned using wheat 90 K and 660 K SNP arrays to identify important herbicide resistance loci. Genome-wide association study (GWAS) revealed 329 significant single-nucleotide polymorphisms (SNPs) with phenotypic variance explained (PVE) of 11.3% to 27.6%. Among these SNPs, 15 were detected in multiple environments and they were mainly distributed on chromosomes 1B, 2D, 5B, 5D, 6D, and 7D. Further analysis indicated that gHR-5B (467-587 Mb), gHR-7D (46-52 Mb), and gHR-1B (517-580 Mb) were important herbicide resistance loci in wheat. Linkage mapping in a bi-parental population detected one QTL (qHR-1B) with PVE of 7.44% to 8.28%. This is reliable locus because its physical position (554-566 Mb) overlapped with gHR-1B by GWAS in the genome of Chinese Spring. This study provided some herbicide-resistant germplasm and important genetic loci for identifying genes of common wheat.

Haynaldia villosa is a wild relative of wheat and a valuable gene resource for wheat improvement. Owing to the limited number of probes available for fluorescence in situ hybridization (FISH), the resolution at which the karyotype of H. villosa can be characterized is poor, hampering accurate characterization of small segmental alien introgressions. We designed ten oligonucleotide probes using tandem repeats in DNA sequences derived from the short arm of H. villosa chromosome 6V (6VS). FISH with seven of them resulted in clear signals on H. villosa chromosomes. Using these, we constructed FISH karyotypes for H. villosa using oligo-6VS-1 and oligo-6VS-35 oligonucleotides and characterized the distribution of the two probes in five different H. villosa accessions. The new FISH probes can efficiently characterize H. villosa introgressions into wheat.