Hon-Ming Lam

Resequencing of 31 wild and cultivated soybean genomes identifies patterns of genetic diversity and selection

We report a large-scale analysis of the patterns of genome-wide genetic variation in soybeans. We re-sequenced a total of 17 wild and 14 cultivated soybean genomes to an average of approximately ×5 depth and >90% coverage using the Illumina Genome Analyzer II platform. We compared the patterns of genetic variation between wild and cultivated soybeans and identified higher allelic diversity in wild soybeans. We identified a high level of linkage disequilibrium in the soybean genome, suggesting that marker-assisted breeding of soybean will be less challenging than map-based cloning. We report linkage disequilibrium block location and distribution, and we identified a set of 205,614 tag SNPs that may be useful for QTL mapping and association studies. The data here provide a valuable resource for the analysis of wild soybeans and to facilitate future breeding and quantitative trait analysis.

Glutamate-receptor genes in plants.

In animal brains, ionotropic glutamate receptors (GluRs) function as glutamate-activated ion channels in rapid synaptic transmission. We have now discovered that genes encoding putative ionotropic GluRs exist in plants, and we present preliminary evidence for their involvement in light-signal transduction. It may be that signalling between cells by excitatory amino acids in animal brains evolved from a primitive signalling mechanism that existed before the divergence of plants and animals. Our findings also help to explain why neuroactive compounds made by plants work on receptors in human brains.

Use of Arabidopsis Mutants and Genes To Study Amide Amino Acid Biosynthesis

Studies of enzymes involved in nitrogen assimilation in higher plants have an impact on both basic and applied plant research. First, basic research in this area should uncover the mechanisms by which plants regulate genes involved in a metabolic pathway. Second, because nitrogen is a rate-limiting element in plant growth (Hageman and Lambert, 1988), it may be possible to increase the yield or improve the quality of crop plants by the molecular or genetic manipulation of genes involved in nitrogen assimilation. Research on nitrogen assimilation into amino acids has been complicated by the fact that some of these reactions are catalyzed by multiple isoenzymes located in distinct subcellular compartments. With traditional biochemical approaches, it has been impossible to sort out the function of each isoenzyme in plant nitrogen metabolism. The discovery that genes for chloroplastic and cytosolic isoenzymes of glutamine synthetase (GS) are expressed in distinct cell types (Edwards et al., 1990; Carvalhoet al., 1992; Kamachi et al., 1992)suggeststhat traditional biochemical studies, which begin with tissue disruption, artificially mix isoenzymes that may not coexist in the same cell type in vivo. Thus, in vitro biochemical methods commonly used to define the rate-limiting enzyme in a pathway in unicellular microorganisms may lead to erroneous interpretations when employed to study plant metabolic pathways. An alternative way to define the in vivo function of a particular isoenzyme or to define a rate-limiting enzyme in a pathway is by mutant analysis, as shown by studies of Escherichia coli and yeast. Plant mutants defective in particular isoenzymes of GS or ferredoxin-dependent glutamate synthase (Fd-GOGAT) have been identified in screens for photorespiratory mutants in Arabidopsis and barley (Somerville and Ogren, 1980,1982; Wallsgrove et al., 1987). More recently, Arabidopsis mutants with alterations in the activity of additional enzymes of nitrogen assimilation have been identified using a screening method that does not depend on a growth phenotype (Schultz and Coruzzi, 1995). The in vivo role of the mutated isoenzyme

Metabolic Regulation of the Gene Encoding Glutamine-Dependent Asparagine Synthetase in Arabidopsis thaliana

Here, we characterize a cDNA encoding a glutamine-dependent asparagine synthetase (ASN1) from Arabidopsis thaliana and assess the effects of metabolic regulation on ASN1 mRNA levels. Sequence analysis shows that the predicted ASN1 peptide contains a purF-type glutamine-binding domain. Southern blot experiments and cDNA clone analysis suggest that ASN1 is the only gene encoding glutamine-dependent asparagine synthetase in A. thaliana. The ASN1 gene is expressed predominantly in shoot tissues, where light has a negative effect on its mRNA accumulation. This negative effect of light on ASN1 mRNA levels was shown to be mediated, at least in part, via the photoreceptor phytochrome. We also investigated whether light-induced changes in nitrogen to carbon ratios might exert a metabolic regulation of the ASN1 mRNA accumulation. These experiments demonstrated that the accumulation of ASN1 mRNA in dark-grown plants is strongly repressed by the presence of exogenous sucrose. Moreover, this sucrose repression of ASN1 expression can be partially rescued by supplementation with exogenous amino acids such as asparagine, glutamine, and glutamate. These findings suggest that the expression of the ASN1 gene is under the metabolic control of the nitrogen to carbon ratio in cells. This is consistent with the fact that asparagine, synthesized by the ASN1 gene product, is a favored compound for nitrogen storage and nitrogen transport in dark-grown plants. We have put forth a working model suggesting that when nitrogen to carbon ratios are high, the gene product of ASN1 functions to re-direct the flow of nitrogen into asparagine, which acts as a shunt for storage and/or long-distance transport of nitrogen.

Overexpression of the ASN1 Gene Enhances Nitrogen Status in Seeds of Arabidopsis

In wild-type Arabidopsis, levels of ASN1 mRNA and asparagine (Asn) are tightly regulated by environmental factors and metabolites. Because Asn serves as an important nitrogen storage and transport compound used to allocate nitrogen resources between source and sink organs, we tested whether overexpression of the major expressed gene for Asn synthetase, ASN1, would lead to changes in nitrogen status in the ultimate storage organ for metabolites—seeds. Transgenic Arabidopsis constitutively overexpressing ASN1 under the cauliflower mosaic virus 35S promoter were constructed (35S-ASN1). In seeds of the 35S-ASN1 lines, three observations support the notion that the nitrogen status was enhanced: (a) elevations of soluble seed protein contents, (b) elevations of total protein contents from acid-hydrolyzed seeds, and (c) higher tolerance of young seedlings when grown on nitrogen-limiting media. Besides quantitative differences, changes in the relative composition of the seed amino acid were also observed. The change in seed nitrogen status was accompanied by an increase of total free amino acids (mainly Asn) allocated to flowers and developing siliques. In 35S-ASN1 lines, sink tissues such as flowers and developing siliques exhibit a higher level of free Asn than source tissues such as leaves and stems, despite significantly higher levels of ASN1 mRNA observed in the source tissues. This was at least partially due to an enhanced transport of Asn from source to sink via the phloem, as demonstrated by the increased levels of Asn in phloem exudates of the 35S-ASN1 plants.

Identification of a novel salt tolerance gene in wild soybean by whole-genome sequencing

Using a whole-genome-sequencing approach to explore germplasm resources can serve as an important strategy for crop improvement, especially in investigating wild accessions that may contain useful genetic resources that have been lost during the domestication process. Here we sequence and assemble a draft genome of wild soybean and construct a recombinant inbred population for genotyping-by-sequencing and phenotypic analyses to identify multiple QTLs relevant to traits of interest in agriculture. We use a combination of de novo sequencing data from this work and our previous germplasm re-sequencing data to identify a novel ion transporter gene, GmCHX1, and relate its sequence alterations to salt tolerance. Rapid gain-of-function tests show the protective effects of GmCHX1 towards salt stress. This combination of whole-genome de novo sequencing, high-density-marker QTL mapping by re-sequencing and functional analyses can serve as an effective strategy to unveil novel genomic information in wild soybean to facilitate crop improvement.

Salt Tolerance in Soybean

Soybean is an important cash crop and its productivity is significantly hampered by salt stress. High salt imposes negative impacts on growth, nodulation, agronomy traits, seed quality and quantity, and thus reduces the yield of soybean. To cope with salt stress, soybean has developed several tolerance mechanisms, including: (i) maintenance of ion homeostasis; (ii) adjustment in response to osmotic stress; (iii) restoration of osmotic balance; and (iv) other metabolic and structural adaptations. The regulatory network for abiotic stress responses in higher plants has been studied extensively in model plants such as Arabidopsis thaliana. Some homologous components involved in salt stress responses have been identified in soybean. In this review, we tried to integrate the relevant works on soybean and proposes a working model to describe its salt stress responses at the molecular level.

Food Supply and Food Safety Issues in China

Food supply and food safety are major global public health issues, and are particularly important in heavily populated countries such as China. Rapid industrialisation and modernisation in China are having profound effects on food supply and food safety. In this Review, we identified important factors limiting agricultural production in China, including conversion of agricultural land to other uses, freshwater deficits, and soil quality issues. Additionally, increased demand for some agricultural products is examined, particularly those needed to satisfy the increased consumption of animal products in the Chinese diet, which threatens to drive production towards crops used as animal feed. Major sources of food poisoning in China include pathogenic microorganisms, toxic animals and plants entering the food supply, and chemical contamination. Meanwhile, two growing food safety issues are illegal additives and contamination of the food supply by toxic industrial waste. Chinas connections to global agricultural markets are also having important effects on food supply and food safety within the country. Although the Chinese Government has shown determination to reform laws, establish monitoring systems, and strengthen food safety regulation, weak links in implementation remain.

Neglecting legumes has compromised human health and sustainable food production

The United Nations declared 2016 as the International Year of Pulses (grain legumes) under the banner ‘nutritious seeds for a sustainable future’. A second green revolution is required to ensure food and nutritional security in the face of global climate change. Grain legumes provide an unparalleled solution to this problem because of their inherent capacity for symbiotic atmospheric nitrogen fixation, which provides economically sustainable advantages for farming. In addition, a legume-rich diet has health benefits for humans and livestock alike. However, grain legumes form only a minor part of most current human diets, and legume crops are greatly under-used. Food security and soil fertility could be significantly improved by greater grain legume usage and increased improvement of a range of grain legumes. The current lack of coordinated focus on grain legumes has compromised human health, nutritional security and sustainable food production.

Biochemical and Molecular Characterization of PvPAP3, a Novel Purple Acid Phosphatase Isolated from Common Bean Enhancing Extracellular ATP Utilization

Purple acid phosphatases (PAPs) play diverse physiological roles in plants. In this study, we purified a novel PAP, PvPAP3, from the roots of common bean (Phaseolus vulgaris) grown under phosphate (Pi) starvation. PvPAP3 was identified as a 34-kD monomer acting on the specific substrate, ATP, with a broad pH range and a high heat stability. The activity of PvPAP3 was insensitive to tartrate, indicating that PvPAP3 is a PAP-like protein. Amino acid sequence alignment and phylogenetic analysis suggest that PvPAP3 belongs to the group of plant PAPs with low molecular mass. Transient expression of 35S:PvPAP3-green fluorescent protein in onion (Allium cepa) epidermal cells verified that it might anchor on plasma membrane and be secreted into apoplast. Pi starvation led to induction of PvPAP3 expression in both leaves and roots of common bean, and expression of PvPAP3 was strictly dependent on phosphorus (P) availability and duration of Pi starvation. Furthermore, induction of PvPAP3 expression was more rapid and higher in a P-efficient genotype, G19833, than in a P-inefficient genotype, DOR364, suggesting possible roles of PvPAP3 in P efficiency in bean. In vivo analysis using a transgenic hairy root system of common bean showed that both growth and P uptake of bean hairy roots from the PvPAP3 overexpression transgenic lines were significantly enhanced when ATP was supplied as the sole external P source. Taken together, our results suggest that PvPAP3 is a novel PAP that might function in the adaptation of common bean to P deficiency, possibly through enhancing utilization of extracellular ATP as a P source.