Showing papers in "Crop Journal in 2017"
TL;DR: The compensatory effect of chitosan in reducing the negative impact of stress conditions on dry matter and oil yield was due mainly to stimulation of osmotic adjustment through proline accumulation and reduction of lipid peroxidase level, which increased the integrity of cell membranes of thyme leaves.
Abstract: Thymus daenensis , a perennial herb, is often grown in areas that experience drought conditions during its growing period. Application of chitosan may compensate for the negative impact of drought stress on the yield of oil and secondary metabolites in Thymus . The interactive effects of foliar application of chitosan and drought stress on dry matter, essential oil yield, and selected physiological characteristics including photosynthetic pigments, osmotic adjustment, and lipid peroxidation of Thymus were investigated in a two-year study from 2014 to 2015. Treatments consisted of 0, 200, and 400 μL L − 1 chitosan applied to plants grown under field capacity, mild drought stress (50% field capacity), and severe drought stress (25% field capacity). Dry matter yield decreased substantially as drought stress intensified. However, essential oil content increased under stress conditions, with the highest essential oil yield obtained from plants under mild drought stress. Foliar application of chitosan compensated to some extent for dry matter and oil yield reduction of plants grown under drought stress. The highest essential oil yield (1.52 g plant − 1 ) was obtained by application of 400 μL L − 1 chitosan under the mild stress condition in 2015 when plants were mature. The compensatory effect of chitosan in reducing the negative impact of stress conditions on dry matter and oil yield was due mainly to stimulation of osmotic adjustment through proline accumulation and reduction of lipid peroxidase level, which increased the integrity of cell membranes of thyme leaves.
218 citations
TL;DR: Drought resistance in the drought-resistant cultivar ‘Changhan 58’ is regulated by stomatal characteristics through a decrease in transpiration rate in order to improve integral WUE and photosynthetic performance, and through sustaining a higher ear photosynthesis rate, therefore enhancing overall drought-resistance.
Abstract: In wheat, the ear is one of the main photosynthetic contributors to grain filling under drought stress conditions. In order to determine the relationship between stomatal characteristics and plant drought resistance, photosynthetic and stomatal characteristics and water use efficiency (WUE) were studied in two wheat cultivars: the drought-resistant cultivar ‘Changhan 58’ and the drought-sensitive cultivar ‘Xinong 9871’. Plants of both cultivars were grown in pot conditions under well-watered (WW) and water-stressed (WS) conditions. In both water regimes, ‘Changhan 58’ showed a significantly higher ear photosynthetic rate with a lower rate of variation and a significantly higher percentage variation of transpiration compared to control plants at the heading stage under WS conditions than did ‘Xinong 9871’ plants. Moreover, ‘Changhan 58’ showed lower stomatal density (SD) and higher stomatal area per unit organ area ( A ) under both water conditions. Water stress decreased SD, A , and stomatal width (SW), and increased stomatal length in flag leaves (upper and lower surfaces) and ear organs (awn, glume, lemma, and palea), with the changes more pronounced in ear organs than in flag leaves. Instantaneous WUE increased slightly, while integral WUE improved significantly in both cultivars. Integral WUE was higher in ‘Changhan 58’, and increased by a greater amount, than in ‘Xinong 9871’. These results suggest that drought resistance in ‘Changhan 58’ is regulated by stomatal characteristics through a decrease in transpiration rate in order to improve integral WUE and photosynthetic performance, and through sustaining a higher ear photosynthetic rate, therefore enhancing overall drought-resistance.
158 citations
TL;DR: This review of the advances and limitations of family-based mapping and natural population- based mapping instead of linkage mapping and association mapping describes statistical methods used for improving detection power and computational speed and outlines emerging areas such as large-scale meta-analysis for genetic mapping in crops.
Abstract: Dissecting the genetic architecture of complex traits is an ongoing challenge for geneticists. Two complementary approaches for genetic mapping, linkage mapping and association mapping have led to successful dissection of complex traits in many crop species. Both of these methods detect quantitative trait loci (QTL) by identifying marker–trait associations, and the only fundamental difference between them is that between mapping populations, which directly determine mapping resolution and power. Based on this difference, we first summarize in this review the advances and limitations of family-based mapping and natural population-based mapping instead of linkage mapping and association mapping. We then describe statistical methods used for improving detection power and computational speed and outline emerging areas such as large-scale meta-analysis for genetic mapping in crops. In the era of next-generation sequencing, there has arisen an urgent need for proper population design, advanced statistical strategies, and precision phenotyping to fully exploit high-throughput genotyping.
148 citations
TL;DR: Moderate AWD with an appropriate nitrogen application rate may exert a synergistic effect on grain yield and result in higher WUE and nitrogen use efficiency and further research is needed to understand root–soil interaction and evaluate the long-term effects of moderate AWD on sustainable agriculture.
Abstract: To meet the major challenge of increasing rice production to feed a growing population under increasing water scarcity, many water-saving regimes have been introduced in irrigated rice, such as an aerobic rice system, non-flooded mulching cultivation, and alternate wetting and drying (AWD). These regimes could substantially enhance water use efficiency (WUE) by reducing irrigation water. However, such enhancements greatly compromise grain yield. Recent work has shown that moderate AWD, in which photosynthesis is not severely inhibited and plants can rehydrate overnight during the soil drying period, or plants are rewatered at a soil water potential of − 10 to − 15 kPa, or midday leaf potential is approximately − 0.60 to − 0.80 MPa, or the water table is maintained at 10 to 15 cm below the soil surface, could increase not only WUE but also grain yield. Increases in grain yield WUE under moderate AWD are due mainly to reduced redundant vegetative growth; improved canopy structure and root growth; elevated hormonal levels, in particular increases in abscisic acid levels during soil drying and cytokinin levels during rewatering; and enhanced carbon remobilization from vegetative tissues to grain. Moderate AWD could also improve rice quality, including reductions in grain arsenic accumulation, and reduce methane emissions from paddies. Adoption of moderate AWD with an appropriate nitrogen application rate may exert a synergistic effect on grain yield and result in higher WUE and nitrogen use efficiency. Further research is needed to understand root–soil interaction and evaluate the long-term effects of moderate AWD on sustainable agriculture.
132 citations
TL;DR: With the application of advanced breeding and production technologies, in the near future, the oil yield and quality of rapeseed varieties will be greatly increased, and more varieties with desirable traits, especially early maturation, high yield, high resistance to biotic and abiotic stress, and suitability for mechanized harvesting will be developed.
Abstract: Rapeseed ( Brassica napus L.) is the largest oilseed crop in China and accounts for about 20% of world production. For the last 10 years, the production, planting area, and yield of rapeseed have been stable, with improvement of seed quality and especially seed oil content. China is among the leading countries in rapeseed genomic research internationally, having jointly with other countries accomplished the whole genome sequencing of rapeseed and its two parental species, Brassica oleracea and Brassica rapa . Progress on functional genomics including the identification of QTL governing important agronomic traits such as yield, seed oil content, fertility regulation, disease and insect resistance, abiotic stress, nutrition use efficiency, and pod shattering resistance has been achieved. As a consequence, molecular markers have been developed and used in breeding programs. During 2005–2014, 215 rapeseed varieties were registered nationally, including 210 winter- and 5 spring-type varieties. Mechanization across the whole process of rapeseed production was investigated and operating instructions for all relevant techniques were published. Modern techniques for rapeseed field management such as high-density planting, controlled-release fertilizer, and biocontrol of disease and pests combined with precision tools such as drones have been developed and are being adopted in China. With the application of advanced breeding and production technologies, in the near future, the oil yield and quality of rapeseed varieties will be greatly increased, and more varieties with desirable traits, especially early maturation, high yield, high resistance to biotic and abiotic stress, and suitability for mechanized harvesting will be developed. Application of modern technologies on the mechanized management of rapeseed will greatly increase grower profit.
124 citations
103 citations
TL;DR: This review summarizes recent progress in understanding the molecular mechanisms of heat tolerance in wheat and discusses integrative strategies to improve heat tolerance by utilization of existing germplasm including modern cultivars, landraces and related species.
Abstract: As a cool season crop, wheat (Triticum aestivum L.) has an optimal daytime growing temperature of 15 °C during the reproductive stage. With global climate change, heat stress is becoming an increasingly severe constraint on wheat production. In this review, we summarize recent progress in understanding the molecular mechanisms of heat tolerance in wheat. We firstly describe the impact of heat tolerance on morphology and physiology and its potential effect on agronomic traits. We then review recent discoveries in determining the genetic and molecular factors affecting heat tolerance, including the effects of phytohormone signaling and epigenetic regulation. Finally, we discuss integrative strategies to improve heat tolerance by utilization of existing germplasm including modern cultivars, landraces and related species.
90 citations
TL;DR: The results suggest that overaccumulation of GB resulting from introduction of the BADH gene can enhance the salt tolerance of transgenic plants, especially in the protection of the components and function of thylakoid membranes, thereby making photosynthesis better.
Abstract: Wheat (Triticum aestivum L.) lines T1, T4, and T6 were genetically modified to increase glycine betaine (GB) synthesis by introduction of the BADH (betaine aldehyde dehydrogenase, BADH) gene from mountain spinach (Atriplex hortensis L.). These transgenic lines and WT of wheat (T. aestivum L.) were used to study the effect of increased GB synthesis on wheat tolerance to salt stress. Salt stress due to 200 mmol L− 1 NaCl impaired the photosynthesis of the four wheat lines, as indicated by declines in net photosynthetic rate (Pn), stomatal conductance (Gs), maximum photochemical efficiency of PSII (Fv/Fm), and actual photochemical efficiency of PSII (ФPSII) and an increase in intercellular CO2 concentration (Ci). In comparison with WT, the effect of salinity on the three transgenic lines was mild. Salt stress caused disadvantageous changes in lipids and their fatty acid compositions in the thylakoid membrane of the transgenic lines and WT. Under salt stress, the three transgenic lines showed slightly higher chlorophyll and carotenoid contents and higher Hill reaction activities and Ca2 +-ATPase activity than WT. All the results suggest that overaccumulation of GB resulting from introduction of the BADH gene can enhance the salt tolerance of transgenic plants, especially in the protection of the components and function of thylakoid membranes, thereby making photosynthesis better. Changes in lipids and fatty acid compositions in the thylakoid membrane may be involved in the increased salt stress tolerance of the transgenic lines.
78 citations
TL;DR: Piriformospora indica- mediated plant protection against the detrimental effects of drought may result from enhanced antioxidant enzyme activity, proline accumulation, and expression of drought-related genes and lower membrane damage in maize plants.
Abstract: Drought stress is one of the most severe environmental constraints to plant growth and crop productivity. Plant growth is greatly affected by drought stress, and plants, to survive, adapt to this stress by invoking different pathways. Piriformospora indica , a root-colonizing endophytic fungus of Sebacinales, promotes plant growth and confers resistance to biotic and abiotic stresses, including drought stress, by affecting the physiological properties of the host plant. The fungus strongly colonizes the roots of maize ( Zea mays L.) and promotes shoot and root growth under both normal growth conditions and drought stress. We used polyethylene glycol (PEG-6000) to mimic drought stress and found that root fresh and dry weight, leaf area, SPAD value, and leaf number were increased in P. indica -colonized plants. The antioxidative activities of catalases and superoxide dismutases were upregulated within 24 h in the leaves of P. indica -colonized plants. Drought-related genes DREB2A , CBL1 , ANAC072 , and RD29A were upregulated in drought-stressed leaves of P. indica -colonized plants. Furthermore, after drought treatment, proline content increased, whereas accumulation of malondialdehyde (MDA), an indicator of membrane damage, decreased in P. indica -colonized maize. We conclude that P. indica- mediated plant protection against the detrimental effects of drought may result from enhanced antioxidant enzyme activity, proline accumulation, and expression of drought-related genes and lower membrane damage in maize plants.
78 citations
TL;DR: Recent progress in resistance QTL identification, candidate functional gene discovery, marker-assisted improvement of FHB resistant varieties, and findings in investigating association of signal molecules with FHB response are presented, with the assistance from rapidly growing genomics platforms.
Abstract: Fusarium head blight (FHB) or scab caused by Fusarium graminearum is a major threat to wheat production in China as well as in the world. To combat this disease, multiple efforts have been carried out internationally. In this article, we review our long-time effort in identifying the resistance genes and dissecting the resistance mechanisms by both forward and reverse genetics approaches in the last two decades. We present recent progress in resistance QTL identification, candidate functional gene discovery, marker-assisted improvement of FHB resistant varieties, and findings in investigating association of signal molecules, such as Ca++, SA, JA, and ET, with FHB response, with the assistance from rapidly growing genomics platforms. The information will be helpful for designing novel and efficient approaches to curb FHB.
74 citations
TL;DR: Results show that oxidative stress can be triggered in finger millet plants by Ni stress by induction of lipoxygenase activity, increase in levels of proline, O 2 •− radical, MDA, and H 2 O 2 , and reduction in the activity of antioxidant enzymes in shoots and roots.
Abstract: This study investigated the effect of salicylic acid (SA) and sodium nitroprusside (SNP; NO donor) on nickel (Ni) toxicity in germinating finger millet seedlings. Fourteen-day-old finger millet plants were subjected to 0.5 mmol L − 1 Ni overload and treated with 0.2 mmol L − 1 salicylic acid and 0.2 mmol L − 1 sodium nitroprusside to lessen the toxic effect of Ni. The Ni overload led to high accumulation in the roots of growing plants compared to shoots, causing oxidative stress. It further reduced root and shoot length, dry mass, total chlorophyll, and mineral content. Exogenous addition of either 0.2 mmol L − 1 SA or 0.2 mmol L − 1 SNP reduced the toxic effect of Ni, and supplementation with both SA and SNP significantly reduced the toxic effect of Ni and increased root and shoot length, chlorophyll content, dry mass, and mineral concentration in Ni-treated plants. The results show that oxidative stress can be triggered in finger millet plants by Ni stress by induction of lipoxygenase activity, increase in levels of proline, O 2 •− radical, MDA, and H 2 O 2 , and reduction in the activity of antioxidant enzymes such as CAT, SOD, and APX in shoots and roots. Exogenous application of SA or SNP, specifically the combination of SA + SNP, protects finger millet plants from oxidative stress observed under Ni treatment.
TL;DR: A positive regulatory role of the auxin-responsive gene TaSAUR75 in plant responses to drought and salt stress is revealed and provide a candidate gene for improvement of abiotic stress tolerance in crop breeding.
Abstract: Small auxin-upregulated RNAs ( SAUR s) are genes regulated by auxin and environmental factors. In this study, we identified a SAUR gene in wheat, TaSAUR75 . Under salt stress, TaSAUR75 is downregulated in wheat roots. Subcellular localization revealed that TaSAUR75 was localized in both the cytoplasm and nucleus. Overexpression of TaSAUR75 increased drought and salt tolerance in Arabidopsis . Transgenic lines showed higher root length and survival rate and higher expression of some stress-responsive genes than control plants under salt and drought stress. Less H 2 O 2 accumulated in transgenic lines than in control plants under drought stress. Our findings reveal a positive regulatory role of the auxin-responsive gene TaSAUR75 in plant responses to drought and salt stress and provide a candidate gene for improvement of abiotic stress tolerance in crop breeding.
TL;DR: Significant changes in signal transduction and metabolic regulation of seed germination involve diverse reactions and complex regulation at different levels of metabolic organization.
Abstract: During germination of barley (Hordeum vulgare L.) seeds, important morphological and physiological changes take place, including development of organs and tissues and activation of metabolic pathways. Germination and dormancy of seeds are regulated by abscisic acid, gibberellins, reactive oxygen species (ROS), reactive nitrogen species (RNS) and several other factors. Activities of ascorbate–glutathione cycle enzymes, responsible for scavenging ROS, strongly increase. Catalase and superoxide dismutase activities, also scavenging ROS, decrease at the onset of seed germination and then increase. With the increase in aerobic metabolism after radicle protrusion, the activities of the fermentation enzymes lactate and alcohol dehydrogenase decline rapidly. The RNS-scavenging activity of S-nitrosoglutathione reductase decreases in the course of seed germination, in concert with elevation of nitric oxide production and protein nitrosylation. This activity supports the role of RNS in regulating seed germination. Transcription of various genes at different phases of seed germination exhibits phase-specific changes. During imbibition, genes involved in cell wall metabolism are highly expressed; in the middle phase of seed germination before radicle protrusion, genes involved in amino acid synthesis, protein synthesis, and transport and nucleic acid synthesis are upregulated significantly, and after radicle protrusion, genes involved in photosynthetic metabolism are induced. In summary, signal transduction and metabolic regulation of seed germination involve diverse reactions and complex regulation at different levels of metabolic organization.
TL;DR: China has remained the world's leading producer of peas, faba beans, mung beans, and adzuki beans in recent decades, as documented by FAO statistics and China Agriculture Statistical Reports.
Abstract: Food legumes comprise all legumes grown for human food in China as either dry grains or vegetables, except for soybean and groundnut. China has a vast territory with complex ecological conditions. Rotation, intercropping, and mixed cropping involving pulses are normal cropping systems in China. Whether indigenous or introduced crops, pulses have played an important role in Chinese cropping systems and made an important contribution to food resources for humans since ancient times. The six major food legume species (pea, faba bean, common bean, mung bean, adzuki bean, and cowpea) are the most well-known pulses in China, as well as those with more local distributions; runner bean, lima bean, chickpea, lentil, grass pea, lupine, rice bean, black gram, hyacinth bean, pigeon pea, velvet bean, winged bean, guar bean, sword bean, and jack bean. China has remained the world's leading producer of peas, faba beans, mung beans, and adzuki beans in recent decades, as documented by FAO statistics and China Agriculture Statistical Reports. The demand for food legumes as a healthy food will markedly increase with the improvement of living standards in China. Since China officially joined the World Trade Organization (WTO) in 2001, imports of pea from Canada and Australia have rapidly increased, resulting in reduced prices for dry pea and other food legumes. With reduced profits for food legume crops, their sowing area and total production has decreased within China. At the same time, the rising consumer demand for vegetable food legumes as a healthy food has led to attractive market prices and sharp production increases in China. Vegetable food legumes have reduced growing duration and enable flexibility in cropping systems. In the future, production of dry food legumes will range from stable to slowly decreasing, while production of vegetable food legumes will continue to increase.
TL;DR: The distribution and ecoregions, origin and domestication, and landmark varieties of several minor cereals in China are described, finding nearly all of the minor cereal species are drought-tolerant and fertilizer-efficient.
Abstract: China is a leading country in the production of several minor cereals such as foxtail millet, Job's tears, naked oat, and naked barley. Sorghum and proso millet have also contributed greatly to Chinese agriculture. Foxtail millet, sorghum, barley, and proso millet were widely grown as major crops 60 years ago, and the reduction in their cultivation area reflects historical changes in Chinese agriculture over the past decades. Systematic germplasm collections from the 1950s to the 1990s gathered more than 66,690 accessions of these minor cereals, and for some of them, the Chinese germplasm collections are the largest in the world; for example, the 27,700 accessions of foxtail millet. Germplasm evaluations of each cereal species have focused mainly on drought tolerance, nutritional quality, and resistance to their main diseases. Comparisons among lines and selection of those with desirable traits were the main breeding methods for minor cereals in the 1950s and 1960s, but these methods were replaced by crossbreeding in the 1970s. Newly developed cultivars have greatly changed the production situation, and many super cultivars have become milestones in crop breeding history. In this review, we describe the distribution and ecoregions, origin and domestication, and landmark varieties of several minor cereals in China. Nearly all of the minor cereals are drought-tolerant and fertilizer-efficient. The requirements for environmentally friendly crops and a more diverse food supply for humans and animals provide new opportunities to cultivate minor cereals in the drier and warmer environmental conditions that are predicted in the future.
TL;DR: Results show that the DTD method is a simple, direct and relatively accurate evaluation method for drought-tolerance breeding of upland rice.
Abstract: Worldwide, approximately 27 million ha of rice are grown in upland rather than paddy fields, and is subject to drought stress. To counter this stress, it is desirable to breed new rice cultivars with improved drought tolerance. For breeding purposes, especially for breeding upland rice, it is desirable to develop a simple and accurate method to evaluate rice drought tolerance. We describe a new method that can be used to evaluate efficiently the drought tolerance degree (DTD) of upland rice cultivars, and call it the DTD method. DTD is defined as the mean of the ratios of green leaf length to total leaf length of the top three leaves in every rice seedling after drought treatment, and thus takes values from zero to one. To test whether the DTD method works effectively to evaluate drought tolerance of upland rice cultivars, we determined the DTD values of 13 upland rice cultivars showing varying degrees of drought tolerance in drought-tolerance trials. The idr1-1 mutant, which displayed the strongest drought tolerance of the 13 cultivars as identified by drought-tolerance trials under severe drought stress, had the highest DTD value and 297-28, displaying the weakest drought tolerance, had the lowest DTD value. Further analyses of water potential, survival rate, panicles per plant, spikelets per panicle, seed setting rate, yield per plant, and contents of proline, chlorophyll, and malondialdehyde (MDA) indicated that DTD values are in general correlated with the values of these traits, making this new method useful for assessing the drought tolerance of upland rice cultivars. These results show that the DTD method is a simple, direct and relatively accurate evaluation method for drought-tolerance breeding of upland rice.
TL;DR: Maize plant architecture with increased tolerance of high densities is probably dependent on the smaller but flatter leaves around the ear, and integration of canopy openness is expected to increase the simulation accuracy of the present model.
Abstract: The size and distribution of leaf area determine light interception in a crop canopy and influence overall photosynthesis and yield. Optimized plant architecture renders modern maize hybrids (Zea mays L.) more productive, owing to their tolerance of high plant densities. To determine physiological and yield response to maize plant architecture, a field experiment was conducted in 2010 and 2011. With the modern maize hybrid ZD958, three plant architectures, namely triangle, diamond and original plants, were included at two plant densities, 60,000 and 90,000 plants ha− 1. Triangle and diamond plants were derived from the original plant by spraying the chemical regulator Jindele (active ingredients, ethephon, and cycocel) at different vegetative stages. To assess the effects of plant architecture, a light interception model was developed. Plant height, ear height, leaf size, and leaf orientation of the two regulated plant architectures were significantly reduced or altered compared with those of the original plants. On average across both plant densities and years, the original plants showed higher yield than the triangle and diamond plants, probably because of larger leaf area. The two-year mean grain yield of the original and diamond plants were almost the same at 90,000 plants ha− 1 (8714 vs. 8798 kg ha− 1). The yield increase (up to 5%) of the diamonds plant at high plant densities was a result of increased kernel number per ear, which was likely a consequence of improved plant architecture in the top and middle canopy layers. The optimized light distribution within the canopy can delay leaf senescence, especially for triangle plants. The fraction of incident radiation simulated by the interception model successfully reflected plant architecture traits. Integration of canopy openness is expected to increase the simulation accuracy of the present model. Maize plant architecture with increased tolerance of high densities is probably dependent on the smaller but flatter leaves around the ear.
TL;DR: It is concluded that variations in environmental conditions (temperature and radiation) during grain filling markedly affect growth rate and duration of grain filling and eventually affect kernel weight and yield of maize.
Abstract: Variation in weather conditions during grain filling has substantial effects on maize kernel weight (KW). The objective of this work was to characterize variation in KW with sowing date-associated weather conditions and examine the relationship between KW, grain filling parameters, and weather factors. Maize was sown on eight sowing dates (SD) at 15–20-day intervals from mid-March to mid-July during 2012 and 2013 in the North China Plain. With sowing date delay, KW increased initially and later declined, and the greatest KW was obtained at SD6 in both years. The increased KW at SD6 was attributed mainly to kernel growth rate (Gmean), and effective grain-filling period (P). Variations in temperature and radiation were the primary factors that influenced KW and grain-filling parameters. When the effective cumulative temperature (AT) and radiation (Ra) during grain filling were 950 °C and 1005.4 MJ m− 2, respectively, P and KW were greatest. High temperatures (daily maximum temperature [Tmax] > 30.2 °C) during grain filling under early sowing conditions, or low temperatures (daily minimum temperature [Tmin] 7.1 °C) decreased kernel growth rate and ultimately final KW. When sowing was performed from May 25 through June 27, higher KW and yield of maize were obtained. We conclude that variations in environmental conditions (temperature and radiation) during grain filling markedly affect growth rate and duration of grain filling and eventually affect kernel weight and yield of maize.
TL;DR: The newly developed genic and genomic SSR markers described in this study will be valuable genomic resources for the assessment of genetic diversity, population structure, evaluation of germplasm accessions, construction of genetic maps, identification of genes of interest, and application of marker-assisted selection in cowpea breeding programs.
Abstract: Cowpea (Vigna unguiculata) is an important legume crop with diverse uses. The species is presently a minor crop, and evaluation of its genetic diversity has been very limited. In this study, a total of 200 genic and 100 genomic simple sequence repeat (SSR) markers were developed from cowpea unigene and genome sequences, respectively. Among them, 27 genic and 27 genomic SSR markers were polymorphic and were used for assessment of genetic diversity and population structure in 105 selected cowpea accessions. A total of 155 alleles and 2.9 alleles per marker were identified, and the average polymorphic information content (PIC) value was 0.3615. The average PIC of genomic SSRs (0.3996) was higher than that of genic SSRs (0.3235), and most of the polymorphic genomic SSRs were composed of di- and trinucleotide repeats (51.9% and 37.0% of all loci, respectively). The low level of detected genetic diversity may be attributed to a severe genetic bottleneck that occurred during the cowpea domestication process. The accessions were classified by structure and cluster analysis into four subgroups that correlated well with their geographic origins or collection sites. The classification results were also consistent with the results from principal coordinate analysis and can be used as a guide during future germplasm collection and selection of accessions as breeding materials for cultivar improvement. The newly developed genic and genomic SSR markers described in this study will be valuable genomic resources for the assessment of genetic diversity, population structure, evaluation of germplasm accessions, construction of genetic maps, identification of genes of interest, and application of marker-assisted selection in cowpea breeding programs.
TL;DR: Analysis of expression correlation and Gene Ontology annotation suggested that OsNF-Y genes were co-expressed with genes that participated in stress, accumulation of seed storage reserves, and plant development, suggesting that NF-Y subunits formed complexes that take part in transcriptional regulation.
Abstract: Nuclear factor Y (NF-Y) is a ubiquitous transcription factor that regulates important physiological and developmental processes. In this study, we identified 34 OsNF-Y genes in rice, including 6 newly identified genes. Expression profile analysis covering the whole life cycle revealed that transcripts of OsNF-Y differentially accumulated in a tissue-specific, preferential or constitutive manner. In addition, gene duplication studies and expression analyses were performed to determine the evolutionary origins of the OsNF-Y gene family. Nine OsNF-Y genes were differentially expressed after treatment of seedlings with one or more abiotic stresses such as drought, salt and cold. Analysis of expression correlation and Gene Ontology annotation suggested that OsNF-Y genes were co-expressed with genes that participated in stress, accumulation of seed storage reserves, and plant development. Co-expression analysis also revealed that OsNF-Y genes might interact with each other, suggesting that NF-Y subunits formed complexes that take part in transcriptional regulation. These results provide useful information for further elucidating the function of the NF-Y family and their regulatory pathways.
TL;DR: It is suggested that an integrated approach combining advances from genetics, physiology, and biotechnology needs to be used for higher precision and efficiency of breeding programs aimed at improving abiotic stress tolerance in both chickpea and pigeonpea.
Abstract: Chickpea (Cicer arietinum L.) and pigeonpea [Cajanus cajan L. (Millsp.)] play an important role in mitigating protein malnutrition for millions of poor vegetarians living in regions of the semi-arid tropics. Abiotic stresses such as excess and limited soil moisture (water-logging and drought), heat and chilling (high and low temperature stresses), soil salinity, and acidity are major yield constraints, as these two crops are grown mostly under rainfed conditions in risk-prone marginal and degraded lands with few or no inputs. Losses due to such stresses vary from 30% to 100% depending on their severity. The literature abounds in basic information concerning screening techniques, physiological mechanisms, and genetics of traits associated with resistance/tolerance to abiotic stresses in these two crops. However, the final outcome in terms of resistant/tolerant varieties has been far from satisfactory. This situation calls for improving selection efficiency through precise phenotyping and genotyping under high-throughput controlled conditions using modern tools of genomics. In this review, we suggest that an integrated approach combining advances from genetics, physiology, and biotechnology needs to be used for higher precision and efficiency of breeding programs aimed at improving abiotic stress tolerance in both chickpea and pigeonpea.
TL;DR: An optimized protocol for the Agrobacterium rhizogenes -mediated transformation of soybean and the induction of hairy root development in vitro is described, which represents an efficient and rapid platform for study of soy bean gene function.
Abstract: Soybean is one of the world's most important oil and protein crops. Efficient transformation is a key factor for the improvement of soybean by genetic modification. We describe an optimized protocol for the Agrobacterium rhizogenes -mediated transformation of soybean and the induction of hairy root development in vitro. Cotyledons with 0.5-cm hypocotyls were cut from 5-day-old seedlings and used as explants. After infection and co-cultivation, hairy roots were produced in induction culture medium after 10–12 days. Using this method, 90%–99% of the infected explants of five different cultivars produced hairy roots within one month. Observations using reporter constructs showed that 30%–60% of the hairy roots induced were transformed. Based on high transformation efficiency and short transformation period, this method represents an efficient and rapid platform for study of soybean gene function.
TL;DR: In this review, the major role of high-affinity potassium transporter genes in enhancing the salt tolerance of wheat is summarized and the link between maintenance of reactive oxygen species (ROS) homeostasis and salt tolerance through a comprehensive study of a wheat introgression line is examined.
Abstract: Wheat is one of the most important food crops, and its yield is seriously restricted by high salinity and other abiotic stresses. Many attempts have been made to elucidate the major physiological processes associated with salt tolerance and to identify the genes controlling the processes. In this review, the major role of high-affinity potassium transporter (HKT) genes in enhancing the salt tolerance of wheat is summarized. The link between maintenance of reactive oxygen species (ROS) homeostasis and salt tolerance through a comprehensive study of a wheat introgression line is examined, and the contribution of a set of genes involved in this process is depicted. New research strategies to uncover the mechanisms underlying salt tolerance in wheat based on recent advances in omics will be discussed.
TL;DR: The novel mutant lines are useful genetic resources for production or future cowpea breeding programs in Namibia or similar environments.
Abstract: This study determined the effects of genotype-by-environment (G × E) interaction and stability of yield among elite cowpea (Vigna unguiculata L.) selections derived by gamma irradiation. The study was conducted in Namibia at three selected sites: Bagani, Mannheim, and Omahenene, during 2014/2015 and 2015/2016. Thirty-four newly developed mutant genotypes and three local checks were evaluated using a randomized complete block design with three replications. Grain yield data were analyzed using the additive main effects and multiplicative interaction (AMMI) and the genotype main effect plus genotype-by-environment interaction (GGE) biplot methods. The AMMI and GGE biplot models explained 77.49% and 75.57% of total observed genotypic variation, respectively. Bagani and Omahenene were the environments best discriminating the test genotypes during 2014/2015 and 2015/2016, respectively. Four promising mutant genotypes: G9 (ShL3P74), G10 (ShR3P4), G12 (ShR9P5), and G4 (ShL2P4), showed wide adaptation and grain yields of 2.83, 2.06, 1.99, and 1.95 t ha− 1, respectively. The novel mutant lines are useful genetic resources for production or future cowpea breeding programs in Namibia or similar environments.
TL;DR: An association-mapping study was conducted using 37,539 Single Nucleotide Polymorphisms (SNPs) to identify genomic regions controlling the heat stress traits and candidate genes in the QTL regions included genes associated with flowering, male sterility, pollen abortion, embryo abortion reducing pollen development, and pod development.
Abstract: High temperatures have a detrimental effect on growth, development, and yield of Brassica napus . Even a short period of heat stress can lead to yield losses of 15%–20%. A collection of spring-type accessions available in Germplasm Resources Information Network (GRIN) were used to assess the effect of short periods of high-temperature stress at the early flowering stage of B. napus . Two sets of accessions with three replications per set were grown in a greenhouse at 22/18 °C day/night temperatures. Plants from the second set at the 6-day flowering stage were exposed to heat-stress conditions (maximum temperature up to 35 °C) in a plant growth chamber for five days. The heat-stressed plants were then allowed to recover in a greenhouse. Pollen sterility, sterile/aborted pods, and number of pods on main raceme were recorded for both control (set 1) and heat stressed (set 2) plants. Heat susceptibility indices for all three traits were calculated and an association-mapping study was conducted using 37,539 Single Nucleotide Polymorphisms (SNPs) to identify genomic regions controlling the heat stress traits. A total of 5, 8, and 7 quantitative trait loci (QTL) were associated with pollen sterility, sterile/aborted pods, and number of pods on main raceme, respectively. Together they explained respectively 46.3%, 60.5%, and 60.6% of phenotypic variation. Candidate genes in the QTL regions included genes associated with flowering, male sterility, pollen abortion, embryo abortion reducing pollen development, and pod development.
TL;DR: This review highlights the available tools and methodologies for wheat functional genomics research developed with the assistance of NGS technology and recent progress, particularly the concerted effort in generating multiple reference genomes, strategies to attain genome-wide genetic variation, genome- wide association studies, mutant population generation, and NGS-supported gene cloning and functional characterization.
Abstract: Bread wheat is not only an important cereal crop but also a model for study of an allopolyploid plant with a large, highly repetitive genome. Advances in next-generation sequencing (NGS) technology provide needed throughput to conquer the enormous size of the wheat genome. Multiple high quality reference genome sequences will soon be available. Full-scale wheat functional genomics studies are dawning. In this review we highlight the available tools and methodologies for wheat functional genomics research developed with the assistance of NGS technology and recent progress, particularly the concerted effort in generating multiple reference genomes, strategies to attain genome-wide genetic variation, genome-wide association studies, mutant population generation, and NGS-supported gene cloning and functional characterization. These resources and platforms lay a solid foundation for wheat research, leading to a new era of wheat functional genomics that will bridge the gap between genotype and phenotype. Dissection of wheat genomes and gene functions should assist in genomics-assisted selection and facilitate breeding of elite varieties for sustainable agriculture in China and the world.
TL;DR: It is indicated that screening for disease resistance requires multi-environment trials, whereas a single-environment trial suffices to screen for total carotene content.
Abstract: General and specific environmental adaptation of genotypes is the main goal of breeders. However, genotype-by-environment (G × E) interaction complicates the identification of genotypes for release. This study aimed at analyzing the effects of G × E interaction on the expression of important cassava traits using two multivariate analyses: additive main effects and multiplicative interaction (AMMI) and genotype stability index (GSI). Total carotene content (TCC), postharvest physiological deterioration (PPD), and reaction to viral diseases were significantly affected by G × E interaction effects. The low percent (%) variation due to genotype for cassava brown streak disease (CBSD) explained the influence of environment on CBSD expression. The % variation due to genotype for TCC was higher (96%) than variation due to environment (1.7%) and G × E interaction (2.4%) indicating a low interaction effect of environment on TCC accumulation. The % variation due to genotype was higher than % variation due to environment for all traits but CBSD root necrosis and CBSD on stems, indicating the influence of environment on the severity of the viral diseases. These findings indicate that screening for disease resistance requires multi-environment trials, whereas a single-environment trial suffices to screen for total carotene content.
TL;DR: Annotation of the SSR-containing unigenes revealed their putative functions in various biological and molecular processes, including responses to biotic and abiotic signals, and suggested these markers can efficiently measure genetic diversity and serve for mapping of quantitative trait loci in jute.
Abstract: Corchorus capsularis (white jute) and C. olitorius (dark jute) are the two principal cultivated species of jute that produce natural bast fiber of commercial importance. We have identified 4509 simple sequence repeat (SSR) loci from 34,163 unigene sequences of C. capsularis to develop a non-redundant set of 2079 flanking primer pairs. Among the SSRs, trinucleotide repeats were most frequent (60%) followed by dinucleotide repeats (37.6%). Annotation of the SSR-containing unigenes revealed their putative functions in various biological and molecular processes, including responses to biotic and abiotic signals. Eighteen expressed gene-derived SSR (eSSR) markers were successfully mapped to the existing single-nucleotide polymorphism (SNP) linkage map of jute, providing additional anchor points. Amplification of 72% of the 74 randomly selected primer pairs was successful in a panel of 24 jute accessions, comprising five and twelve accessions of C. capsularis and C. olitorius , respectively, and seven wild jute species. Forty-three primer pairs produced an average of 2.7 alleles and 58.1% polymorphism in a panel of 24 jute accessions. The mean PIC value was 0.34 but some markers showed PIC values higher than 0.5, suggesting that these markers can efficiently measure genetic diversity and serve for mapping of quantitative trait loci (QTLs) in jute. A primer polymorphism survey with parents of a wide-hybridized population between a cultivated jute and its wild relative revealed their efficacy for interspecific hybrid identification. For ready accessibility of jute eSSR primers, we compiled all information in a user-friendly web database, JuteMarkerdb ( http://jutemarkerdb.icar.gov.in /) for the first time in jute. This eSSR resource in jute is expected to be of use in characterization of germplasm, interspecific hybrid and variety identification, and marker-assisted breeding of superior-quality jute.
TL;DR: Sowing later than normal could increase lodging resistance while maintaining grain yield and NUE, and the increase in UTE offset the reduction in UPE, resulting in equal NUEs among all sowing dates.
Abstract: Lodging resistance of winter wheat (Triticum aestivum L.) can be increased by late sowing. However, whether grain yield and nitrogen use efficiency (NUE) can be maintained with delayed sowing remains unknown. During the 2013–2014 and 2014–2015 growing seasons, two winter wheat cultivars were sown on three dates (early sowing on October 1, normal sowing on October 8, and late sowing on October 15) to investigate the responses of lodging resistance, grain yield, and NUE to sowing date. No significant differences in lodging resistance, grain yield, or NUE between early and normal sowing were observed. Averaging over the two cultivars and years, postponing the sowing date significantly increased lodging resistance by 53.6% and 49.6% compared with that following early and normal sowing, respectively. Lodging resistance was improved mainly through a reduction in the culm height at the center of gravity and an increase in the tensile strength of the base internode. Late sowing resulted in similar grain yield as well as kernel weight and number of kernels per square meter, compared to early and normal sowing. Averaging over the two cultivars and years, delayed sowing resulted in a reduction in nitrogen uptake efficiency (UPE) by 11.0% and 9.9% compared to early and normal sowing, respectively, owing to reduced root length density and dry matter accumulation before anthesis. An average increase in nitrogen utilization efficiency (UTE) of 12.9% and 11.2% compared to early and normal sowing, respectively, was observed with late sowing owing to a reduction in the grain nitrogen concentration. The increase in UTE offset the reduction in UPE, resulting in equal NUEs among all sowing dates. Thus, sowing later than normal could increase lodging resistance while maintaining grain yield and NUE.
TL;DR: The features and functions of CCT genes in cereal crops are reviewed and future research to focus on C CT genes and their utilization in crop breeding are proposed.
Abstract: Control of flowering time is crucial for reproductive success of cereal crops, and has a significant impact on grain yield as well as adaptation to diverse environmental conditions Plants integrate signals from both environmental cues and endogenous regulatory pathways to fine-tune flowering time The CCT domain originally described to a 43-amino acid sequence at the C-terminus of three Arabidopsis proteins, namely CONSTANS (CO), CO-LIKE, and TIMING OF CAB1 (TOC1) The CCT domain-containing genes ( CCT genes), which encode transcription co-factors, are the major genetic determinants that modulate flowering time, and this in turn enables plants to effectively expand their territory to take advantage of favorable habitats Moreover, certain CCT genes have pleiotropic effects on morphological traits and confer resistance/tolerance to biotic/abiotic stresses CCT genes can be classified into three families, namely COL ( CONSTANS - like ), PRR ( Pseudo - response regulator ), and CMF ( CCT motif family ), based on their non-CCT domains During domestication, natural and artificial selection resulted in reduced nucleotide diversity of CCT genes in modern cultivated cereals than their wild types Here, we review the features and functions of CCT genes in cereal crops and propose future research to focus on CCT genes and their utilization in crop breeding