Based on known cDNAs of rice starch synthase isoforms, we constructed dsRNA interference vectors for starch synthase I (SSI) to produce transgenic plants containing starch with a moderately high amylose content. We investigated the effect of SSI suppression on grain quality traits, starch biosynthesis, and amylopectin chain distribution in rice plants exposed to two different temperature regimes. The activities and transcripts of BEs, DBEs, and other SS isoforms were further investigated to clarify the effect of SSI suppression on these key enzymes and their specific isoforms under different temperature treatments. Suppression of SSI by RNAi altered grain starch component and amylopectin chain distribution, but it exerted only a slight effect on total starch content (%) and accumulation amount (mg kernel⁻¹) and on starch granule morphology and particle size distribution. Under normal temperature (NT), insignificant differences in kernel weight, chalky kernel proportion, chalky degree, and starch granule morphology between SSI-RNAi line and its wild type (WT) were observed. However, amylose content (AC) level and granule-bound starch synthase (GBSS) activity in rice endosperms were markedly increased by SSI-RNAi suppression. The chalky kernel proportion and chalky degree of SSI-RNAi lines were significantly higher than those of WT under high temperature (HT) exposure at filling stage. Inhibition of SSI by RNAi affected amylopectin chain distribution and raised starch gelatinization temperature (GT) in two ways: directly from the SSI deficiency itself and indirectly by reducing BEIIb amounts in an SSI-deficient background. The deficiency of SSI expression led to an alteration in the susceptibility of grain chalkiness occurrence and starch gelatinization temperature to HT exposure, owing to a pleiotropic effect of SSI deficiency on the expression of other genes associated with starch biosynthesis.

Grain weight is one of the most important determinants of grain yield in rice. In this study, QTL analysis for grain weight, grain length, and grain width was performed using populations derived from crosses between major parental lines of three-line indica hybrid rice. A total of 27 QTL for grain weight were detected using three recombinant inbred line populations derived from the crosses Teqing/IRBB lines, Zhenshan 97/Milyang 46, and Xieqingzao/Milyang 46. Of these, 10 were found in only a single population and the other 17 in two or all three populations. Nine of the 17 common QTL were located in regions where no QTL associated with grain weight have been cloned and one was selected for fine-mapping. Eight populations segregating in an isogenic background were derived from one F₇ residual heterozygote of Teqing/IRBB52. The target QTL, qTGW10-20.8 controlling grain weight, grain length, and grain width, was localized to a 70.7-kb region flanked by InDel markers Te20811 and Te20882 on the long arm of chromosome 10. The QTL region contains seven annotated genes, of which six encode proteins with known functional domains and one encodes a hypothetical protein. One of the genes, Os10g0536100 encoding the MIKC-type MADS-box protein OsMADS56, is the most likely candidate for qTGW10-20.8. These results provide a basis for cloning qTGW10-20.8, which has an important contribution to grain weight variation in rice.

Hexaploid triticale (×Triticosecale, AABBRR) is an important forage crop and a promising energy plant. Transferring D-genome chromosomes or segments from common wheat (Triticum aestivum) into hexaploid triticale is attractive in improving its economically important traits. Here, a hexaploid triticale 6D(6A) substitution line Lin 456 derived from the cross between the octoploid triticale line H400 and the hexaploid wheat Lin 56 was identified and analyzed by genomic in situ hybridization (GISH), fluorescence in situ hybridization (FISH), and molecular markers. The GISH analysis showed that Lin 456 is a hexaploid triticale with 14 rye (Secale cereale) chromosomes and 28 wheat chromosomes, whereas non-denaturing fluorescence in situ hybridization (ND-FISH) and molecular marker analysis revealed that it is a 6D(6A) substitution line. In contrast to previous studies, the signal of Oligo-pSc119.2 was observed at the distal end of 6DL in Lin 456. The wheat chromosome 6D was associated with increased grain weight and decreased spikelet number using the genotypic data combined with the phenotypes of the F₂ population in the three environments. The thousand-grain weight and grain width in the substitution individuals were significantly higher than those in the non-substitution individuals in the F₂ population across the three environments. We propose that the hexaploid triticale 6D(6A) substitution line Lin 456 can be a valuable and promising donor stock for genetic improvement during triticale breeding.

Sharp eyespot, mainly caused by the soil-borne fungus Rhizoctonia cerealis, affects wheat (Triticum aestivum L.) production worldwide. In this study, we isolated TaCML36 gene encoding a wheat calmodulin-like protein, and studied its defense role in protection against R. cerealis. Transcription of TaCML36 was significantly elevated by both R. cerealis infection and exogenous ethylene treatment. Transcription was higher in resistant wheat lines than in susceptible ones. There were copies of TaCML36 on chromosomes 5A, 5B, and 5D. The TaCML36 protein is composed of 183 amino acids and contains two calcium-binding EF-hand domains. Subcellular localization assays in wheat indicated that TaCML36 localizes in both the cytoplasm and nucleus. Virus-induced gene silencing and disease assessment indicated that compared to the controls, TaCML36-silenced wheat plants displayed significantly reduced resistance to R. cerealis and had greater fungal biomass, suggesting that knockdown of TaCML36 impaired host resistance. Knockdown of TaCML36 also significantly repressed expression of pathogenesis-related genes such as Chitinase 1, PDF35, and PR17C, the ethylene response factor-encoding gene TaPIE1, and ethylene biosynthesis gene ACO2. Collectively, our results suggest that TaCML36 positively participates in the innate immune response to R. cerealis infection by modulating expression of defense-associated genes possibly in the ethylene signaling pathway.

Fiber length of cotton (Gossypium hirsutum L.) decreases under drought stress, potassium (K) could diminish the decreased caused by drought, but the mechanism associated with this alleviation effect is not clear. We evaluated the effect of K on fiber elongation using two cotton cultivars, Simian 3 and Siza 3, grown in well-watered and drought-stressed conditions. Potassium fertilizer (K₂O) was applied 0, 150, or 300?kg?ha⁻¹ in each growing condition. Drought stress reduced the final fiber length due to a decline in the maximum rate of rapid elongation (V_max, mm?day⁻¹). The application of K alleviated the drought-induced fiber length reduction by increasing V_max. At 10 and 15?days post-anthesis (DPA), drought significantly reduced osmotic potential (OP) and increased K⁺ and malate contents at all K rates, relative to well-watered conditions, which was associated with increased activities of phosphoenolpyruvate carboxylase (PEPC), V-ATPase, PPase, and PM H⁺-ATPase in cotton fiber. However, the relative contribution of K⁺ and malate to OP declined under drought in comparison with well-watered condition. Compared with control without K, K application decreased OP and increased the accumulation of osmolytes (K⁺, malate and soluble sugar) as well as the activities of related enzymes in fiber irrespective of water treatments. Moreover, K application increased osmotic adjustment during drought, and improved the contribution of K⁺ and malate to OP, especially under drought stress. This study showed that drought decreased fiber length by reducing V_max, and K application ameliorates the decline in fiber elongation due to drought by enhancing osmolytes accumulation and their contribution to OP in fiber cells.

Improving water use efficiency (WUE) is an important subject in agricultural irrigation for alleviating the scarcity of water resources in semiarid regions of the North China Plain. Moreover, glycine betaine (GB) is one of the most effective compatible solutes synthesized naturally in plants for enhancing stress tolerance under abiotic stress, but little information is available on the involvement of GB in regulating crop WUE under field conditions. This study was conducted to explore the role of exogenously applied GB in improving WUE and plant physiological and biochemical responses in winter wheat subjected to conventional or limited irrigation during the 2015-2016 and 2016-2017 growing seasons. Exogenous application of GB significantly enhanced antioxidant enzyme activities and reduced the accumulation of malondialdehyde and hydrogen peroxide under limited irrigation conditions. Furthermore, GB-treated plants maintained higher leaf relative water content and membrane stability, which led to higher chlorophyll content and gas exchange attributes for better intrinsic and instantaneous water use efficiencies compared to control plants under limited irrigation conditions. GB-treated plants had higher indole-acetic acid and zeatin riboside levels but lower ABA levels compared to control plants under conventional and limited irrigation conditions. Additionally, GB enhanced the grain filling rate and duration, grain number per spike, and final grain weight, which resulted in higher grain yield compared to the control. Interestingly, GB significantly improved the integrative and photosynthetic WUE under conventional and limited irrigation conditions, although GB treatment did not markedly affect total water consumption. These results suggest the involvement of GB in improving WUEs in winter wheat by modulating hormonal balance, membrane stability, photosynthetic performance and antioxidant systems to maintain higher grain yield under conventional and limited irrigation conditions.

Soybean (Glycine max [L.] Merr.) is an important source of human dietary protein and vegetable oil. A strong negative correlation between protein and oil contents has hindered efforts to improve soybean seed quality. The metabolic and genetic bases of soybean seed composition remain elusive. We evaluated metabolic diversity in a soybean near-isogenic line (NIL) population derived from parents (JD12 and CMSD) with contrasting seed oil contents. Using GC-TOF/MS, we compared seed primary metabolites of high protein/low oil lines, low protein/high oil lines, and their parents. Principal-components analysis showed that metabolic profiles of all progeny lines could be discriminated based on protein and oil contents. Univariate analysis revealed wide variation and transgressive segregation of metabolites in the population. Twenty-eight annotated metabolites, in particular free asparagine, free 3-cyanoalanine, and L-malic acid, were correlated with seed protein content or seed oil content or seed protein and oil content. These results shed light on the metabolic and genetic basis of soybean seed composition.

Beach pea or beach cowpea (Vigna marina (Burm.) Merr.) belongs to the family Fabaceae. It is a close relative of cultivated Vigna species such as adzuki bean (V. angularis), cowpea (V. unguiculata), mung bean (V. radiata), and blackgram (V. mungo), and is distributed throughout the tropics. With its ability to tolerate salt stress, beach pea has great potential to contribute salt-tolerance genes for developing salt-tolerant cultivars in cultivated Vigna species. However, it is still underutilized in Vigna breeding programs. A draft genome sequence of beach pea was generated using a high-throughput next-generation sequencing platform, yielding 23.7 Gb of sequence from 79,929,868 filtered reads. A de novo genome assembly containing 68,731 scaffolds gave an N50 length of 10,272?bp and the assembled sequences totaled 365.6?Mb. A total of 35,448 SSRs, including 3574 compound SSRs, were identified and primer pairs for most of these SSRs were designed. Genome analysis identified 50,670 genes with mean coding sequence length 1042?bp. Phylogenetic analysis revealed highest sequence similarity with V. angularis, followed by V. radiata. Comparison with the V. angularis genome revealed 16,699 SNPs and 2253 InDels and comparison with the V. radiata genome revealed 17,538 SNPs and 2300 InDels. To our knowledge this is the first draft genome sequence of beach pea derived from an accession (ANBp-14-03) adapted locally in the Andaman and Nicobar Islands of India. The draft genome sequence may facilitate the genetic enhancement in cultivated Vigna species.

The glume is an organ of the maize spikelet and plays important roles in anther and kernel development. Vestigial glume1 (Vg1) is a classic mutant associated with ligule and glume development. Here we report the phenotypic characterization, fine mapping, and candidate gene analysis of the Vg1 mutant. Vg1 is a semi-dominant and pleiotropic gene, and also affects plant height, ear height, and tassel length. Vg1 ligule degeneration begins at the first leaf, and the Vg1 tassel and ear can be distinguished from those of wild-type plants when their lengths reach respectively 55?mm and 51?mm. Using a BC₃ mapping population of 11,445 plants, we delimited the Vg1 functional site to an interval of 7.4?kb, flanked by the markers InDelLM and CRM6. A putative cyclopropane fatty-acid synthase gene (ZmCPA-FAS1) was hypothesized to underlie the mutant phenotype. We detected a Helitron insertion in the sixth intron of ZmCPA-FAS1. Its presence caused abnormal alternative splicing of ZmCPA-FAS1 that conferred new characteristics on the Vg1 mutant. These findings are a basis for further discovery of the molecular mechanism underlying glume development and a potential guide for maize breeding of small-glume varieties, especially sweet corn breeding.

Soybean cyst nematode (SCN) is a highly destructive pathogen. The soybean host genome harbors at least two major genes for resistance (rhg1 and Rhg4), as well as a minor locus (SCN3-11). In the present study, a splicing site in GmSNAP11, the potential causal gene of SCN3-11, was identified by comparison of the GmSNAP11 cDNA sequences generated from resistant and susceptible soybean accessions. The sequence information was used to design a codominant CAPS marker, GmSNAP11-2565, which was used to genotype a panel of 209 soybean accessions varying with respect to SCN resistance. Analyses of the effect of the haplotypes formed by GmSNAP11-2565 and another large-effect (nonsynonymous) locus, GmSNAP11-2307, previously identified in GmSNAP11, revealed linkage disequilibrium (P?<?0.0001) between the two loci, suggesting that GmSNAP11-2565 could be used as a marker for GmSNAP11. GmSNAP11-2565 was accordingly used, along with established markers for GmSNAP18 (rhg1) and GmSHMT (Rhg4), to characterize the panel accessions. The mean SCN female index of accessions carrying only the GmSNAP11 allele associated with resistance (20.3%) was higher than that associated with accessions carrying alleles for resistance at both GmSNAP11 and GmSNAP18 (12.4%), while the index for accessions carrying alleles for resistance at all of GmSNAP11, GmSNAP18, and GmSHMT was very low (1.9%). Selection on all three markers was effective for maintaining a high level of resistance to SCN race 3.

Increasing rice yield potential is a continuous challenge posed by world population growth. To increase yield potential, favorable alleles of valuable genes need to be accumulated in promising germplasm. We conducted comparative yield trials for two years in Tsukuba, Japan, in a temperate region and at the International Rice Research Institute (IRRI), Philippines, in a tropical region using five high-yielding rice cultivars: Takanari and Hokuriku193, developed in Japan, and IR64, NSIC Rc158, and YTH183, developed in the Philippines. Genotype plus genotype × environment interaction (GGE) biplot analysis across four environments (two regions × two seasons) classified the five cultivars into four categories: Takanari and YTH183 showed high adaptability to both tropical and temperate regions, Hokuriku193 was suitable for temperate regions, NSIC Rc158 was suitable for the tropics, and IR64 was inferior to the other cultivars in both regions. The high yield and adaptability in Takanari and YTH183 were attributed to their large sink capacity with good grain filling. The plant type for high yield was different, however, between the two cultivars; Takanari was a panicle-weight type, whereas YTH183 was a panicle-number type. Evaluations of F₂ progeny of a cross between Takanari and YTH183 showed transgressive segregation for number of panicles per plant as well as number of spikelets per panicle, leading some F₂ plants to produce more spikelets per plant (corresponding to larger sink size) than the parental cultivars in both regions. These results suggest the possibility of developing rice cultivars with high yield potential in both temperate and tropical regions by crossing temperate with tropical high-yielding cultivars.

Number of pods per plant and number of seeds per pod are quantitative, multigenic traits and important components of yield in soybean [Glycine max (L.) Merr.]. Pods are distributed unevenly in the upper, middle, and lower segments of the plant and this distribution is affected by sowing date (SD). A population of four-way recombinant inbred lines (FW-RIL), containing 160 F_2:8 individuals, was generated from the cross (Kenfeng 14?×?Kenfeng 15)?×?(Heinong 48?×?Kenfeng 19). A linkage map consisting of 275 simple sequence repeat (SSR) markers was used to map quantitative trait loci (QTL) associated with the production of one, two, three, and four seeds per pod in the upper, middle, and lower segments of plants at two SDs, totaling 12 measurements per SD. A wide range of variation in the twelve characteristics was observed among the four parental lines and the FW-RIL population at the two SDs. The effect of SD2 (May 17, 2016) on pod number was stronger than that of SD1 (May 7, 2016) because the heritability of each trait in the SD1 experiment was generally greater than that of SD2. The study identified 76 QTL controlling pod number, with the phenotypic variation explained by each QTL ranging from 1.86% to 13.71%. The numbers of QTL controlling one, two, three, and four seeds per pod were 28, 23, 23, and 23, respectively. There were 30, 28, and 28 QTL controlling the pod number in the upper, middle, and lower segments of the plant, respectively. Forty-five QTL were identified at SD1 and 38 QTL were identified at SD2. Seventeen QTL were associated with pod-number traits. The QTL qPN-A1-3 was associated with the number of pods containing one seed in the middle segment of the plant at both SDs. Sixty-three QTL were published QTL (common areas existed when integrating on a map GmComposite2003 of Wm82 based on left and right markers). and 13 QTL related to pod number were newly discovered. These results provide a reference for breeders to improve soybean yield by combining advantageous alleles for these QTL. Future studies may reveal candidate genes for these QTL and identify causal alleles for marker-assisted selection.

Rice (Oryza sativa L.) is a major food crop worldwide. Plant height and yield are important agronomic traits of rice. Several genes regulating plant height and/or yield have been cloned. However, the molecular mechanisms coordinating plant height and yield are not fully characterized. Here, we report a novel gene, OstMAPKKK5 that encodes a truncated variant of a mitogen-activated protein kinase kinase kinase 5 (OsMAPKKK5) lacking an intact kinase domain. Transgenic plants overexpressing OstMAPKKK5 in indica cultivar 9311 showed increased plant height, grain length, grain width, 1000-grain weight, grain number per main panicle, and yield. Real-time quantitative PCR showed that OstMAPKKK5 was widely expressed in various tissues and developmental stages. The increased plant height and yield were attributed to enlarged cell size. Overexpression of OstMAPKKK5 led to higher contents of various forms of endogenous gibberellin (GA), especially the most common active forms, GA₁, GA₃, GA₄. We concluded that OstMAPKKK5 positively regulates plant height and yield in rice by affecting cell size, and that its underlying mechanism is based on increased endogenous GA content.