The characterization of agronomically important genes has great potential for the improvement of wheat. However, progress in wheat genetics and functional genomics has been impeded by the high complexity and enormous size of the wheat genome. Recent advances in genome sequencing and sequence assembly have produced a high-quality genome sequence for wheat. Here, we suggest that the strategies used to characterize biological mechanisms in model species, including mutant preparation and characterization, gene cloning methods, and improved transgenic technology, can be applied to wheat biology. These strategies will accelerate progress in wheat biology and promote wheat breeding program development. We also outline recent advances in wheat functional genomics. Finally, we discuss the future of wheat functional genomics and the rational design-based molecular breeding of new wheat varieties to contribute to world food security.

Soybean cyst nematode (SCN, Heterodera glycines Ichinohe) is the most economically damaging disease of soybean worldwide, and breeding host plant resistance is the most feasible option for SCN management. In this review, we summarise the progress made so far in identifying nematode-resistance genes, the currently available sources of resistance, possible mechanisms of SCN resistance and strategies for soybean breeding. To date, only two sources of SCN resistance have been widely used, from the accessions PI 88788 and Peking, which has resulted in a shift in SCN resistance and created a narrow genetic base for SCN resistance. These resistant germplasms for SCN are classified into two types according to their copy number variation in a 31-kb genomic region: PI 88788-type resistance requires high copy numbers of a rhg1 resistance allele (rhg1-b) and Peking-type resistance requires both low copy numbers of a different rhg1 resistance allele (rhg1-a) and a resistant allele at another locus, Rhg4. Resistance related to rhg1 primarily involves impairment of vesicle trafficking through disruption of soluble NSF-attachment protein receptor (SNARE) complexes. By contrast, resistance via Rhg4 involves disturbance of folate homeostasis at SCN feeding sites due to alteration of the enzymatic activity of serine hydroxymethyltransferase (SHMT). Other potential mechanisms, including plant defences mediated by salicylic acid (SA) and jasmonic acid (JA) signalling modulation, have also been suggested for SCN resistance. Indeed, genome-wide association studies (GWAS) have identified other candidate SCN resistance genes, such as GmSNAP11. Although gene functional analysis in a transient expression system could increase the efficiency of candidate gene identification, information on novel genes and mechanisms for SCN resistance remains limited. Any beneficial candidate genes identified might, when fully exploited, be valuable for improving the efficiency of marker-assisted breeding and dissecting the molecular mechanisms underlying SCN resistance.

Sucrose non-fermenting-1-related protein kinase-1 (SnRK1) regulates carbon and nitrogen metabolism in plants. However, its roles and their underlying mechanisms in tolerance to abiotic stresses are little known. The present study indicated that the IbSnRK1 gene was strongly induced by NaCl, polyethylene glycol (PEG) 6000, hydrogen peroxide (H₂O₂), cold (4 °C), and abscisic acid (ABA). Its overexpression significantly increased salt, drought, and cold tolerance in transgenic sweet potato plants. ABA, proline, and K⁺ contents were significantly increased, whereas malondialdehyde (MDA), Na⁺ and H₂O₂ contents and O₂⁻ production rate were significantly decreased in the transgenic plants under salt, drought, and cold stresses. Overexpression of the gene up-regulated genes involved in ABA biosynthesis, stress response, and stomatal closure; increased enzyme activities in the reactive oxygen species (ROS) scavenging system; and controlled stomatal closure under salt, drought, and cold stresses. These results show that the IbSnRK1 gene confers salt, drought, and cold tolerance in sweet potato by activating the ROS scavenging system and controlling stomatal closure via the ABA signaling pathway.

The mesocotyl, a structure located between the basal part of the seminal root and the coleoptile node of seedlings, contributes to pushing the shoot tip through the soil surface, a function that is essential for the uniform emergence of direct-seeded rice. Its elongation is inhibited by light and induced in darkness. This investigation of an indica rice (P25) with vigorous mesocotyl elongation was aimed at identifying the “omics” basis of its light-induced growth inhibition. A transcriptomic comparison between mesocotyl tissues that had developed in the dark and then been exposed to light identified many differentially expressed genes (DEGs) and differentially abundant microRNAs (miRNAs). Degradome sequencing analysis revealed 27 negative miRNA-target pairs. A co-expression regulatory network was constructed based on the miRNAs, their corresponding targets, and DEGs with a common Gene Ontology term. It suggested that auxin and light, probably antagonistically, affect mesocotyl elongation by regulating polyamine oxidase activity.

Cotton (Gossypium hirsutum) is an important fiber crop worldwide. Insect attack causes cotton yield and quality losses. However, little is known about the mechanism of cotton response to insect attack. We simulated insect feeding by applying insect oral secretions (OS) to wounds, and combined transcriptome and metabolome analysis to investigate how OS from two major pest species (Helicoverpa armigera and Spodoptera litura) affect cotton defense responses. We found that respectively 12,668 and 13,379 genes were differentially expressed in comparison with wounding alone. On addition of OS, the jasmonic acid signaling pathway was rapidly and strongly induced, whereas genes involved in salicylic acid biosynthesis were downregulated. On constructing a coexpression gene network, we identified a hub gene encoding a leucine-rich repeat receptor kinase that may play an important role in early signal recognition and transduction. OS from the two insect species altered the abundance of flavonoid-related compounds in different patterns. Gossypol remained in lower concentration after OS application than after wounding alone, suggesting a suppressive effect of OS on cotton defense response. This study illustrated transcriptional and metabolic changes of cotton in responding to OS from two chewing insect species, identified potential key response genes, and revealed evidence for OS inhibition of wounding-induced cotton defense response.

The TaGS3 homoeologous genes (homoeologs) located on chromosomes 7A, 4A, and 7D in hexaploid wheat were cloned. Relative expression analysis of the three TaGS3 homoeologs revealed that the expression levels of TaGS3-4A and TaGS3-7D in developing grains were higher than that of TaGS3-7A. Genetic evidence showed that TaGS3 was a negative regulator of grain weight and grain size. Fifteen polymorphic sites and five haplotypes were detected in TaGS3-4A. Two molecular markers were developed to distinguish the five haplotypes. Association analysis using 260 accessions from Chinese wheat mini-core collection (MCC) indicated that TaGS3-4A affected thousand grain weight (TGW) and grain length (GL). HAP-4A-1 and HAP-4A-2 were favorable haplotypes that increased TGW and GL and had undergone strong selection during domestication of wheat. In addition, interaction of the TaGS3-4A and TaGS3-7D homoeologs had significant additive effects on the grain traits. Hap-4A-1/Hap-7D-2 was the best haplotype combination in increasing TGW and GL. The frequencies and geographic distributions of favorable TaGS3 haplotypes among 1388 wheat accessions from worldwide sources provided clues for selection of yield-related traits. Our findings demonstrated that TaGS3-4A had significant effects on TGW and GL. Marker-assisted selection of HAP-4A-1/2 combined with HAP-7D-2 has potential to increase wheat yields.

Lentil (Lens culinaris Medikus subsp. culinaris, 2n = 14) is a cool-season legume with high production potential for multiple uses. However, limited molecular research has been conducted in this species owing to its large genome, which impedes the generation of genome sequences and the development of molecular markers. In this study, more than 1.37 billion filtered clean reads were collected by RNA-Seq of six diverse lentil accessions and 217,836 transcripts and 161,095 unigenes were de novo assembled, yielding respectively 257.1 and 240.6 million nucleotides. The mean transcript length was 1180 bp and the N50 and N90 lengths were respectively 2075 and 479 bp. The mean length of the unigenes was 1494 bp and their N50 and N90 values were respectively 2203 and 714 bp. The unigenes were annotated against seven databases. The FLOWERING LOCUS T (FT) gene homolog in lentil showed high protein sequence similarity to the FT gene homologs of pea and alfalfa. On the basis of the RNA-Seq analysis, 26,449 EST-SSR markers were designed in silico, and 276 preliminarily screened markers were selected to evaluate polymorphism in 94 diverse lentil accessions. In total, 125 (45.29%) of 276 EST-SSR markers were found to be polymorphic. A total of 130,073 SNP loci were detected and 78 (61.41%) of 127 SNPs were successfully converted to KASP markers. Population genetic analyses of the lentil accessions with EST-SSR and KASP markers revealed similar genetic structures, suggesting that the RNA-Seq-generated resources and the developed markers are reliable for use in molecular marker-assisted breeding of lentil.

Global warming is limiting availability of water resources in arid and semi-arid regions, and so understanding water use efficiency (WUE) is increasingly important for agricultural production in those areas. As China is the largest cotton producing area, the problem of balancing WUE and efficient cotton production is a major issue. In this study, we used a natural population of 517 Upland cotton accessions to conduct a water-controlled trial in south and north of Xinjiang over two years. A total of 18 traits including agronomic traits, fiber yield indices and fiber quality indices, were investigated for broad-sense heritability and coefficient of variation. Appropriate water limitation was found to promote the establishment of favorable agronomic traits in cotton, associated with an increased cotton yield of 8.46% in Xinjiang, at the expense of a certain degree of fiber quality, such as decreased fiber length and an over-higher micronaire value. We detected 33 QTL related to response to water limitation using a drought resistance coefficient (DRC), and 6 QTL were found using a comprehensive indicator of CIDT (comprehensive index of drought tolerance) at the genetic level by integrating resequencing data. Two novel QTL-hotspots including six differentially expressed genes (DEGs) were further identified related to the drought response of cotton. These findings not only suggested a new approach to irrigation of cotton fields in Xinjiang, but also provided abundant genetic evidence for genetic breeders to study drought improvement of crops.

Drought stress is an important factor affecting soybean yield. Improving drought tolerance of soybean varieties can increase yield and yield stability when the stress occurs. Identifying QTL related to drought tolerance using molecular marker-assisted selection is able to facilitate the development of drought-tolerant soybean varieties. In this study, we used a high-yielding and drought-sensitive cultivar ‘Zhonghuang 35’ and a drought-tolerant cultivar ‘Jindou 21’ to establish F_6:9 recombinant inbred lines. We constructed a high-density genetic map using specific locus amplified fragment sequencing (SLAF-Seq) technology. The genetic map contained 8078 SLAF markers distributing across 20 soybean chromosomes with a total genetic distance of 3780.98 cM and an average genetic distance of 0.59 cM between adjacent markers. Two treatments (irrigation and drought) were used in the field tests, the Additive-Inclusive Composite Interval Mapping (ICIM-ADD) was used to call QTL, and plant height and seed weight per plant were used as the indicators of drought tolerance. We identified a total of 23 QTL related to drought tolerance. Among them, seven QTL (qPH2, qPH6, qPH7, qPH17, qPH19-1, qPH19-2, and qPH19-3) on chromosomes 2, 6, 7, 17, and 19 were related to plant height, and five QTL (qSWPP2, qSWPP6, qSWPP13, qSWPP17, and qSWPP19) on chromosomes 2, 6, 13, 17, and 19 were related to seed weight and could be considered as the major QTL. In addition, three common QTL (qPH6/qSWPP6, qPH17/qSWPP17, and qPH19-3/qSWPP19) for both plant height and seed weight per plant were located in the same genomic regions on the same chromosomes. Three (qPH2, qPH17, and qPH19-2) and four novel QTL (qSWPP2, qSWPP13, qSWPP17, and qSWPP19) were identified for plant height and seed weight per plant, respectively. Two pairs of QTL (qPH2/qSWPP2 and qPH17/qSWPP17) were also common for both plant height and seed weight per plant. These QTL and closely linked SLAF markers could be used to accelerate breeding for drought tolerant cultivars via MAS.

To investigate the effect of nitrogen management on the grain-filling characteristics and yield formation of maize cultivars with contrasting nitrogen efficiencies, and to identify differences in grain-filling characteristics and yield of maize cultivars in response to nitrogen management, a two-year field experiment was conducted in southwest China in 2015-2016. The grain-filling rate and duration of the N-inefficient cultivar XY 508 were higher than those of the N-efficient cultivar ZH 311. The 100-kernel weight of XY 508 was significantly higher than that of ZH 311. The kernel number per ear of ZH 311 was significantly higher than that of XY 508, making the population filling rate of ZH 311 significantly higher than that of XY 508. The higher population filling rate of the N-efficient maize cultivar led to a significant yield advantage over the N-inefficient maize cultivar. Nitrogen management effectively improved maize grain yield, but the response of maize cultivars with contrasting nitrogen efficiencies to nitrogen management was inconsistent. A basal fertilizer ratio 60.43% with a topdressing ratio 39.57% effectively increased grain-filling rate, delayed the time to maximum filling rate, prolonged the active filling period and effective grain-filling time, increased the 100-kernel weight, and maintained higher kernels per ear, thereby improving the population filling rate and maximizing the yield advantage of the N-efficient cultivar. A 100% basal fertilizer ratio not only increased the number of kernels per ear, but also maintained high grain filling characteristics to obtain a higher 100-kernel weight and increased the population filling rate, leading to a high grain yield in the N-inefficient cultivar. Thus, the 100% basal fertilizer ratio partially compensated for the deficient grain yield of the N-inefficient cultivar.

Fusarium crown rot (FCR), a chronic and severe disease caused by various Fusarium species, is prevalent in semi-arid cropping regions worldwide. One of the major QTL conferring FCR resistance was detected on chromosome arm 1HL (Qcrs.cpi-1H) in barley. To develop markers that can be reliably used to incorporate the resistance locus into breeding programs, we developed and assessed a near-isogenic line-derived population consisting of 1180 recombinant inbred lines targeting the locus. Using this population, we delineated Qcrs.cpi-1H into an interval of 0.4 cM covering a physical length of about 487 kb. Six markers co-segregating with this locus were generated. Co-linearity for genes located in this interval between the genome of barley and those of either rice or Brachypodium distachyon is poor. Three genes with non-synonymous variations between the resistant and susceptible lines were identified within the interval. The results reported in this study not only provide markers for integrating Qcrs.cpi-1H into breeding programs, but also form a solid foundation for cloning the causal gene(s) underlying this locus.

Most modern wheat cultivars were selected on the basis of yield-related indices measured under optimal fertilizer and irrigation inputs. With climate change, land degradation and salinity caused by sea water encroachment, wheat is increasingly subjected to environmental stress. Moreover, expanding urbanization increasingly encroaches upon prime agricultural land in countries like China, and alternative cropping areas must be found. Some of these areas have moderate constraining factors, such as salinity. Therefore, it is important to investigate whether current genetic materials and breeding procedures are maintaining adequate variability to address future problems caused by abiotic stress. In this study, a panel of 307 wheat accessions, including local landraces, exotic cultivars used in Chinese breeding programs and Chinese cultivars released during different periods since 1940, were subjected to a genome-wide association study to dissect the genetic basis of salinity tolerance. Both marker-based and pedigree-based kinship analyses revealed that favorable haplotypes were introduced in some exotic cultivars as well as a limited number of Chinese landraces from the 1940s. However, improvements in salinity tolerance during modern breeding are not as obvious as that of yield. To broaden genetic diversity for increasing salt tolerance, there is a need to refocus attention on local landraces that have high degrees of salinity tolerance and carry rare favorable alleles that have not been exploited in breeding.

DREBs are transcription factors that regulate abiotic stress tolerance in plants. Previously, we reported that wheat transgenic lines overexpressing GmDREB1 showed increased tolerance to drought and salt stress. However, the molecular basis of increased tolerance is still poorly understood, and whether the overexpression of DREB will cause unexpected effects is also of concern. We performed seed metabolic profiling of the genetically modified (GM) wheat T349 and three non-GM cultivars with LC-MS to identify the metabolic basis of stress tolerance and to assess the unexpected effects of exogenous gene insertion. Although we did not note the appearance of novel metabolites or the disappearance of existing metabolites, overexpression of the transcription factor GmDREB1 in T349 wheat influenced metabolite levels in seeds. Increased levels of stress tolerance-associated metabolites were found in the stress-sensitive non-transgenic acceptor counterpart J19, while metabolites associated with cell membrane structure and stability accumulated in T349. Among these metabolites in T349, most showed levels similar to those in the non-GM wheats. Overexpression of GmDREB1 in T349 may cause a shift in its metabolic profile leading to down-regulation of several energy-consuming processes to favor increased yield under stress conditions, which is a reasonable expectation of breeders while creating the GM wheat and GmDREB1 overexpression did not cause unexpected effects in T349 seeds. These results may be helpful for GM crop research and risk assessment.

Photosynthesis is the fundamental basis of plant growth and development, and the improvement of photosynthetic efficiency can therefore promote increased crop yields. In this study, a comparative analysis of photosynthetic physiology and transcriptome was conducted between the high photosynthetic efficient variety BN207 and its parents BN64 and ZM16. The higher chlorophyll fluorescence, chlorophyll and carotenoid contents, and Lhcb1 protein accumulation in BN207 improved photosynthetic efficiency by promoting light energy absorption and conversion. Chloroplasts being distributed more closely to the cell membrane and the higher Rubisco enzyme activity of BN207 enhanced carbon assimilation, resulting in more carbohydrate accumulation in BN207. Transcriptome analysis revealed that there were several key genes mediating the high photosynthetic efficiency of BN207: TraesCS5D02G364100 (chlorophyllase), BGI_novel_G006617 (lycopene ɛ-cyclase), TraesCS4A02G034800 and TraesCS4A02G035100 (Zeaxanthin epoxidase), TraesCS6B02G122500 (light-harvesting complex II chlorophyll a/b binding protein 1). These genes improved the photosynthetic efficiency of BN207 mainly by reducing chlorophyll degradation, promoting carotenoid synthesis, and increasing Lhcb1 protein accumulation. These findings provide important background information for the cultivation of wheat varieties with high photosynthetic efficiency.

Root hairs are fast growing, ephemeral tubular extensions of the root epidermis that aid nutrient and water uptake. The aim of the present study was to identify QTL for root hair length (RHL) using 227 F₈ recombinant inbred lines (RILs) derived from a cross of Zhou 8425B (Z8425B) and Chinese Spring (CS), and to develop convenient molecular markers for marker-assisted breeding in wheat. Analysis of variance of root hair length showed significant differences (P < 0.01) among RILs. The genetic map for QTL analysis consisted of 3389 unique SNP markers. Using composite interval mapping, four major QTL (LOD > 2.5) for RHL were identified on chromosomes 1B (2), 2D and 6D and four putative QTL (2 ≤ LOD ≤ 2.5) were detected on chromosomes 1A, 3A, 6B, and 7B, explaining 3.32%-6.52% of the phenotypic variance. The positive alleles for increased RHL of QTL on chromosomes 2D, 6B and 6D (QRhl.cau-2D, qRhl.cau-6B, and QRhl.cau-6D) were contributed by Z8425B, and CS contributed positive QTL alleles on chromosomes 1A (qRhl.cau-1A), 1B (QRhl.cau-1B.1 and QRhl.cau-1B.2), 3A (qRhl.cau-3A) and 7B (qRhl.cau-7B). STARP markers were developed for QRhl.cau-1B.1, QRhl.cau-2D, QRhl.cau-6D, and qRhl.cau-7B. Haplotype and association analysis indicated that the positive allele of QRhl.cau-6D had been strongly selected in Chinese wheat breeding programs. Collectively, the identified QTL for root hair length are likely to be useful for marker-assisted selection.

Rice planthoppers, including brown planthopper (BPH) and white-backed planthopper (WBPH), are the most destructive pests in Asian rice cultivation regions. Planthopper resistance genes that have been mapped and characterized advance our understanding of underlying resistance mechanisms and facilitate the breeding of resistant varieties, thereby contributing to an efficient pest management strategy. In this study, a novel resistance gene Bph38 derived from the wild rice species Oryza rufipogon Griff. was found to confer high resistance to BPH and WBPH. Conventional mapping was performed to identify regions associated with BPH and WBPH resistance, and two mapping efforts led to the same region on chromosome 4 flanked by markers RM16563 and RM16763. Bulked-segregant analysis and next-generation sequencing were performed using the same population to detect the resistance gene. Conventional mapping narrowed the region to a 12.3-Mb segment, and fine mapping using BC₁F₂ recombinants identified a 79-kb segment flanked by markers YM112 and YM190. Near-isogenic lines (NILs) carrying Bph38 in the 9311 (indica) and BR54 (japonica) genetic backgrounds were developed by crossing and backcrossing with marker-assisted selection. The agronomic traits and BPH and WBPH resistance of the NILs were similar to those of the recurrent parents. Mandatory feeding and host-choice tests revealed that Bph38 showed both antibiotic and antixenotic effects in both insects, with stronger effects in indica-background lines. Further fine mapping and characterization of the major gene may result in map-based cloning of the gene and allow its application in breeding insect-resistant rice varieties.

Husk number (HN) and husk length (HL) influence the mechanical harvesting of maize grain. We investigated the genetic basis of HN and HL using a population of 204 recombinant inbred lines phenotypically evaluated in five environments. The two husk traits showed broad phenotypic variation and high heritability. Nine stable quantitative trait loci (QTL) were identified by single-environment mapping, comprising four QTL for HN and five for HL, and three QTL explained >10% of the phenotypic variation. Joint mapping revealed 22 additive QTL and 46 epistatic QTL. Both additive and epistatic (additive × additive) effects as well as a few large-effect QTL and some minor-effect QTL appeared to contribute to the genetic architecture of HN and HL. The QTL for HN located on chromosome 7, qHN7, which accounted for ~20% of phenotypic variation, was detected in all five environments. qHN7 was fine-mapped to a 721.1 kb physical region based on the maize B73 RefGen_v3 genome assembly. Within this interval, four genes associated with plant growth and development were selected as candidate genes. The results will be useful for improvement of maize husk traits by molecular breeding and provide a basis for the cloning of qHN7.

High temperature (HT) during grain filling is one of the most important environmental factors limiting maize yield and grain quality. Nitrogen (N) fertilizer is essential for maintaining normal plant growth and defense against environmental stresses. The effects of three N rates and two temperature regimes on the grain yield and quality of fresh waxy maize were studied using the hybrids Suyunuo 5 (SYN5) and Yunuo 7 (YN7) as materials. N application rates were 1.5, 4.5, and 7.5 g plant⁻¹, representing low, moderate, and high N levels (LN, MN, and HN, respectively). Mean day/night temperatures during the grain filling of spring- and summer-sown plants were 27.6/21.0°C and 28.6/20.0°C for ambient temperature (AT) and 35/21.0°C and 35/20.0°C for HT, respectively. On average, HT reduced kernel number, weight, yield, and moisture content by 29.8%, 17.9%, 38.7%, and 3.3%, respectively. Kernel number, weight, yield, moisture, and starch contents were highest under MN among the three N rates under both temperature regimes. HT reduced grain starch content at all N levels. HT increased grain protein content, which gradually increased with N rate. Mean starch granule size under MN was larger (10.9 μm) than that under LN and HN (both 10.4μm) at AT. However, the mean size of starch granules was higher under LN (11.7μm) and lower under MN (11.2μm) at HT. Iodine binding capacity (IBC) was lowest under MN and highest under HN among the three N levels under both temperature regimes. In general, IBC at all N rates was increased by HT. Peak viscosity (PV) was gradually reduced with increasing N rate at AT. In comparison with LN, PV was increased by MN and decreased by HN at HT. Retrogradation percentage gradually increased with N rate at AT, but was lowest under MN among the three N rates at HT. LN+AT and MN+HT produced grain with high pasting viscosity and low retrogradation tendency. MN application could alleviate the negative effects of HT on the grain yield and quality of fresh waxy maize.