Common bacterial blight (CBB) is associated with common bean (Phaseolus vulgaris L.), an important grain legume for human consumption worldwide. The disease, caused by Xanthomonas spp. is spread mainly through seed. This paper focuses on the diversity of X. axonopodis pv. phaseoli and X. fuscans subsp. fuscans and interactions between related bacteria and the bean host. Review has suggested that the diversity and taxonomic studies of these pathogens are not exhaustive, especially in areas where detailed molecular analysis has not been conducted and previous characterizations were based on phenotypic features and PCR-based techniques. Also, no study has confirmed differential pathogenicity on bean genotypes based on compatible versus incompatible reactions. However, isolates react differently to wild and domesticated bean sources of resistance in common bean genetic backgrounds. A systematic approach will be required to investigate global changes in gene expression among different sources of resistance in a common bean background. The bacterial isolates that cause CBB should be functionally characterized using genotypes containing major quantitative trait loci (QTL) for CBB resistance. These studies will increase understanding of resistance and how it is manipulated by pathogens.

Wheat high-molecular-weight glutenin subunits (HMW-GS) determine dough elasticity and play an essential role in processing quality. HMW-GS are encoded by Glu-1 genes and controlled primarily at transcriptional level, implemented through the interactions between cis-acting elements and trans-acting factors. However, transcriptional mechanism of Glu-1 genes remains elusive. Here we made a comprehensive analysis of cis-regulatory elements within 1-kb upstream of the Glu-1 start codon (−1000 to −1) and identified 30 conserved motifs. Based on motif distribution pattern, three conserved cis-regulatory modules (CCRMs), CCRM1 (−300 to −101), CCRM2 (−650 to −400), and CCRM3 (−950 to −750), were defined, and their functions were characterized in wheat stable transgenic lines transformed with progressive 5′ deletion promoter::GUS fusion constructs. GUS staining, qPCR and enzyme activity assays indicated that CCRM2 and CCRM3 could enhance the expression level of Glu-1, whereas the 300-bp promoter (−300 to −1), spanning CCRM1 and core region (−100 to −1), was enough to ensure accurate Glu-1 initiation at 7?days after flowering (DAF) and shape its spatiotemporal expression pattern during seed development. Further transgenic assays demonstrated that CCRM1-2 (−300 to −209) containing Complete HMW Enhancer (−246 to −209) was important for expression level but had no effect on expression specificity in the endosperm. In contrast, CCRM1-1 (−208 to −101) was critical for both expression specificity and level of Glu-1. Our findings not only provide new insights to uncover Glu-1 transcription regulatory machinery but also lay foundations for modifying Glu-1 expression.

Grain hardness is an important parameter for wheat quality. To understand the role of glycolipids in the formation of grain hardness, the glycolipid contents in wholegrain wheat flour and the starch granule surfaces of oven-dried and freeze-dried hard and soft wheat grain were analyzed. Changes in endosperm structure and amyloplast membrane integrity during grain development were also examined by electron microscopy. The monogalactosyldigylcerol (MGDG) and digalactosyldigylcerol (DGDG) contents of the starch surface were significantly higher in soft wheat than in hard wheat, regardless of the drying method or developmental stage. Throughout grain development, MGDG content was significantly higher in the starch surface of freeze-dried hard wheat than in the starch surface of oven-dried hard wheat. In contrast, the MGDG content of the starch surface was significantly higher in freeze-dried soft grain at 14 and 35 days after anthesis. No significant difference was observed in puroindoline protein (PIN) accumulation in wholegrain flour from wheat that was dried using the two methods, whereas PIN accumulation on the starch surface of freeze-dried grain was lower than that on the starch surface of oven-dried grain. The gap between the amyloplast membrane and starch granules was larger in hard wheat than in soft wheat, as shown by transmission electron microscopy. For the same wheat cultivar, this gap was larger for oven-dried than for freeze-dried grain. The content of polar lipids in the starch surface was closely related to grain hardness, and the breakdown of the amyloplast membrane may determine the location of polar lipids on the starch surface.

Knowledge of allelic frequencies at loci associated with kernel weight and effects on kernel weight-related traits is crucial for yield improvement in wheat. Kernel weight-related traits were evaluated in 200 Chinese winter wheat cultivars (lines) grown at the Xinxiang Experimental Station, Chinese Academy of Agricultural Sciences, Xinxiang in Henan Province, for three consecutive years from 2014 to 2016. Alleles associated with kernel weight at nine loci, TaCKX6-D1, TaCwi-A1, TaCWI-4A, TaGS1a, TaGS5-A1, TaGS3-3A, TaGW2-6A, TaSus2-2B, and TaTGW6-A1, were determined for all cultivars (lines). ANOVA showed that genotypes, years and their interactions had significant effects on thousand-kernel weight (TKW), kernel length (KL) and kernel width (KW). The overall mean frequencies of alleles conferring high and low TKW at the nine loci were 65.9% and 33.4%, with the ranges of 37.0%-85.0% and 13.5%-63.0% for single loci. The frequencies of high-TKW alleles were over 50.0% at eight of the loci. Genotypes at each locus with the high-TKW allele had higher TKW than those with the low-TKW allele. The high-TKW allele Hap-H at the TaSus2-2B locus can be preferably used to increase grain yield due to its high TKW (49.32?g). A total of 18 main allelic combinations (ACs) at nine loci were detected. Three ACs (AC1-AC3) had significantly higher TKW than AC6 with high-TKW alleles at all nine loci even though they contained some low-TKW alleles. This indicated that other loci controlling kernel weight were present in the high-TKW cultivars. This work provides important information for parental selection and marker-assisted selection for breeding.

Aphanomyces root rot (ARR) of field pea (Pisum sativum), caused by Aphanomyces euteiches, can cause severe root damage, wilting, and large yield losses under wet soil conditions. To identify ways to manage this disease, the effect of A. euteiches inoculum density on field pea was studied under greenhouse and field conditions in 2015 and 2016. Increases in inoculum density reduced seedling emergence, root nodulation, and plant vigor, and resulted in increased root rot severity in both field and greenhouse tests. Seed treatments with the fungicides Apron Advance (thiabendazole?+?fludioxonil?+?metalaxyl)?+?Vibrance (difenoconazole?+?metalaxyl-M?+?sedaxane), INTEGO Solo (ethaboxam), BAS 516F (boscalid?+?pyraclostrobin), BAS 720F (metalaxyl?+?pyraclostrobin?+?fluxapyroxad), and BAS 516F?+?BAS 720F (3:1) were evaluated for their efficacy against ARR. All seed treatments except Apron Advance?+?Vibrance reduced root rot severity under controlled conditions. BAS 516F, BAS 720F and INTEGO Solo improved plant vigor and all treatments reduced seedling blight to varying degrees under greenhouse conditions, but not in the field. A collection of 22 pea genotypes was evaluated for resistance to root rot in field plot experiments. Line 00-2067 showed the least severe root rot symptoms, whereas ‘Spring D’ showed the lowest reduction in yield. The results suggest that there may be an opportunity to combine partial host resistance and fungicidal seed treatments to adequately manage ARR of field pea.

The endosperm plays essential roles in embryogenesis and seed germination and provides abundant resources for human food and industrial products. Identification of genes regulating the development of the endosperm and elucidation of their functions is of great importance for maize genetics and breeding. This study showed that the gene-specific imprinted gene, ETHYLENE-INSENSITIVE 2-like (EIN2-like), is maternally expressed in both endosperm and embryo. The maternally expressed pattern was maintained throughout later seed developmental stages. Bisulfite sequencing using DNA obtained from hybrid endosperm tissues showed that the upstream regions of the alleles of EIN2-like were highly methylated at symmetrical sites (CG and CHG). A differentially methylated region in the upstream part of the maternal allele of EIN2-like was identified and found to be hypomethylated. Expression analysis showed that EIN2-like was highly expressed in the maize endosperm as well as at different stages of cell differentiation (8-12 days after pollination) in the hybrid endosperm. These results suggest that the maternally expressed gene EIN2-like may play crucial roles in the regulation of seed development.

Bulked-segregant analysis coupled with next-generation sequencing (BSA-seq) has emerged as an efficient tool for genetic mapping of single genes or major quantitative trait loci controlling (agronomic) traits of interest. However, such a mapping-by-sequencing approach usually relies on deep sequencing and advanced statistical methods. Application of BSA-Seq based on construction of reduced-representation libraries and allele frequency analysis permitted anchoring the barley pale-green (pg) gene on chromosome 3HL. With further marker-assisted validation, pg was mapped to a 3.9?Mb physical-map interval. In the pg mutant a complete deletion of chlorophyllide a oxygenase (HvCAO) gene was identified. Because the product of this gene converts Chl a to Chl b, the pg mutant is deficient in Chl b. An independent Chl b-less mutant line M4437_2 carried a nonsynonymous substitution (F263L) in the C domain of HvCAO. The study demonstrates an optimized pooling strategy for fast mapping of agronomically important genes using a segregating population.

Non-specific lipid transfer proteins (nsLTPs) are small, basic proteins that are characterized by an eight-cysteine motif. The biological functions of these proteins have been reported to involve plant reproduction and biotic or abiotic stress response. With the completion of the barley genome sequence, a genome-wide analysis of nsLTPs in barley (Hordeum vulgare L.) (HvLTPs) will be helpful for understanding the function of nsLTPs in plants. We performed a genome-wide analysis of the nsLTP gene family in barley and identified 70 nsLTP genes, which can be divided into five types (1, 2, C, D, and G). Each type of nsLTPs shares similar exon and intron gene structures. Expression analysis showed that barley nsLTPs have diverse expression patterns, revealing their various roles. Our results shed light on the phylogenetic relationships and potential functions of barley nsLTPs and will be useful for future studies of barley development and molecular breeding.

Environmental stresses severely impair cotton production worldwide. To identify the genetic basis of, and molecular markers associated with, environmental stresses such as salt, cold and Verticillium wilt, association mapping of salt-, cold-, and disease-tolerance traits was performed in a population of 503 upland cotton accessions using 179 polymorphic SSR markers and 11,975 array-derived SNP markers. Salt and cold tolerance was evaluated via the relative germination rate (RGR) of the seeds under seven and four environments, respectively. The disease index of Verticillium wilt was investigated for two years in the field in Xinjiang. These three traits showed large variation across environments. A genome-wide association study revealed that 31, 19, and 15 SSR markers were associated with RGR-Salt (the relative germination rates of seeds under salt stress), RGR-Cold (the relative germination rates of seeds under cold stress), and DIV (the disease index of Verticillium wilt), respectively. Six SNPs in seven environments and two SNPs in BLUP (best linear unbiased prediction) results were associated with RGR-Salt, and the phenotypic variance explained ranged from 3.96 to 5.00%. Two SNPs (i02237Gh, i02243Gh) on D01 were concluded to be stable genetic loci associated with RGR-Salt. A total of 223 genes were found in a candidate gene interval (D01, 37771-1942912). Of these four genes, GhPIP3A, GhSAG29, GhTZF4, and GhTZF4a, showed expression changes in sensitive and tolerant genotype accessions under salt stress, and were assigned as candidate genes associated with RGR-Salt. This study revealed the genetic basis of stress resistance in upland cotton and will facilitate stress-resistance breeding in cotton.

Besides leaves, non-foliar green organs such as stem and spike are also considered photosynthetic organs. To assess the photosynthetic contributions of these organs, the correlations between these photosynthetic areas and single-spike weight were investigated in a winter wheat (Triticum aestivum L.) under four nitrogen and mulching treatments: N120, N150, N195, and N195?+?M. Two-year repeated field experiments were conducted on the Loess Plateau of China. Non-foliar photosynthetic area, grain-filling ratio and duration, grain yield, and in particular, single-spike weight, were measured, recorded and analyzed. Under the N195?+?M treatment, plants showed the largest area of photosynthetic organs (flag leaf and non-foliar organs) and the highest grain yield and single spike weight. Single-spike weight was positively correlated with the areas of all examined non-foliar photosynthetic organs, in particular with the area above the flag leaf node (R²?=?0.761^?) and the area above the exposed part of the peduncle (EXP) (R²?=?0.800^??). In addition, single-spike weight was highly correlated with average grain-filling ratio (R²?=?0.993^??), whereas it was less highly correlated with grain-filling duration (R²?=?0.533). The morphological traits of non-foliar photosynthetic organs were also more highly correlated with average grain-filling ratio than with average grain-filling duration. The significant correlation between each of the morphological traits (area, length and width) of EXP and single-spike weight indicates that morphological traits of EXP are important in determining spike weight in the Loess Plateau environment.

Agronomically optimizing the timing and rates of nitrogen (N) fertilizer application can increase crop yield and decrease N loss to the environment. Wheat (Triticum aestivum L.)-peanut (Arachis hypogaea L.) relay intercropping systems are a mainstay of economic and food security in China. We performed a field experiment to investigate the effects of N fertilizer on N recovery efficiency, crop yield, and N loss rate in wheat-peanut relay intercropping systems in the Huang-Huai-Hai Plain, China during 2015-2017. The N was applied on the day before sowing, the jointing stage (G30) or the booting stage (G40) of winter wheat, and the anthesis stage (R1) of peanut in the following percentage splits: 50-50-0-0 (N1), 35-35-0-30 (N2), and 35-0-35-30 (N3), using 300?kg?N?ha⁻¹, with 0?kg?N?ha⁻¹ (N0) as control. ¹⁵N-labeled (20.14?atom %) urea was used to trace the fate of N in microplots. The yields of wheat and peanut increased by 12.4% and 15.4% under the N2 and N3 treatments, relative to those under the N1 treatment. The ¹⁵N recovery efficiencies (¹⁵NRE) were 64.9% and 58.1% for treatments N2 and N3, significantly greater than that for the N1 treatment (45.3%). The potential N loss rates for the treatments N2 and N3 were 23.7% and 7.0%, significantly lower than that for treatment N1 (30.1%). Withholding N supply until the booting stage (N3) did not reduce the wheat grain yield; however, it increased the N content derived from ¹⁵N-labeled urea in peanuts, promoted the distribution of ¹⁵N to pods, and ultimately increased pod yields in comparison with those obtained by topdressing N at jointing stage (N2). In comparison with N2, the N uptake and N recovery efficiency (NRE) of N3 was increased by 12.0% and 24.1%, respectively, while the apparent N loss decreased by 16.7%. In conclusion, applying N fertilizer with three splits and delaying topdressing fertilization until G40 of winter wheat increased total grain yields and NRE and reduced N loss. This practice could be an environment-friendly N management strategy for wheat-peanut relay intercropping systems in China.

The Q gene in common wheat encodes an APETALA2 (AP2) transcription factor that causes the free threshing attribute. Wheat spikelets bearing several florets are subtended by a pair of soft glumes that allow free liberation of seeds. In wild species, the glumes are tough and rigid, making threshing difficult. However, the nature of these “soft glumes”, caused by the domestication allele Q is not clear. Here, we found that over expression of Q in common wheat leads to homeotic florets at glume positions. We provide phenotypic, microscopy, and marker genes evidence to demonstrate that the soft glumes of common wheat are in fact lemma-like organs, or so-called sterile-lemmas. By comparing the structures subtending spikelets in wheat and other crops such as rice and maize, we found that AP2 genes may play conserved functions in grasses by manipulating vestigial structures, such as floret-derived soft glumes in wheat and empty glumes in rice. Conversion of these seemingly vegetative organs to reproductive organs may be useful in yield improvement of crop species.

Pre-harvest aflatoxin contamination occurs in maize following kernel colonization by Aspergillus flavus. Aflatoxin contamination resistance is a highly desired trait in maize breeding programs. The identification of novel sources of resistance to pre-harvest aflatoxin contamination is a major focus in germplasm screening efforts. Here, we performed a field evaluation of 64 inbred lines over two years for pre-harvest aflatoxin contamination. Topcrosses were also performed with two testers, B73 and Mo17, to generate 128?F₁ hybrids which were also evaluated over two years. Hybrid performance was used to calculate both general combining ability (GCA) of the inbreds, and observed heterosis for aflatoxin resistance. Over both years of the study, aflatoxin concentrations ranged from 80?±?47 to 17,617?±?8816?μg?kg⁻¹ for inbreds, and from 58?±?39 to 2771?±?780?μg?kg⁻¹ for hybrids with significant variation between years and lines. The inbred lines CML52, CML69, CML247, GT-603, GEMS-0005, Hi63, Hp301, and M37?W showed <1000?μg?kg⁻¹ of aflatoxin accumulation in both years of the study and less than the resistant check, Mp313E, in at least one season. Among these, CML52, GT-603, and Hi63 also showed significant GCA with the testers in hybrid progeny. CML52, GT-603, and M37?W also showed heterotic effects of −13.64%, −12.47%, and?−?24.50%, respectively, with B73 resulting in reduced aflatoxin contamination. GT-603 also showed a similar heterotic effect for aflatoxin contamination, −13.11%, with Mo17 indicating that this line may serve as a versatile source of aflatoxin contamination resistance in breeding programs.