Molecular studies of enhanced apical dominance of phytochrome B mutant sorghum

Light is one of the environmental signals that regulate axillary shoot development. However, little is known about molecular and physiological mechanisms regulating the development of the axillary shoot in response to light signals. Molecular events associated with the enhanced apical dominance of phytochrome B mutant sorghum (Sorghum bicolor) were analyzed to reveal processes mediating axillary shoot development in response to light. The enhanced apical dominance of phyB-1 mutant sorghum is due to inhibition of bud outgrowth and is accompanied by upregulation of the dormancy-associated gene (SbDRM1) in the buds. Increased expression of the Teosinte Branched1 (SbTB1) gene (encoding a putative transcription factor that represses bud outgrowth) suggests that the inhibition of bud outgrowth in phyB-1 sorghum is due to the absence of active phyB to repress SbTB1. The results were confirmed by growing wild type seedlings at high plant density or with supplemental farred (FR) light that induces enhanced apical dominance. However, the SbTB1 gene is not involved in the inhibition of bud outgrowth induced by defoliation in wild type seedlings. The results indicate variations in molecular mechanisms among different signals inhibiting branching. Increased expression of SbMAX2 (which encodes an F-box protein that represses bud outgrowth) in buds repressed by light and defoliation suggests common mechanisms at the downstream end of pathways inhibiting branching. The expression levels of several cell cycle-related genes including SbPCNA, SbHis4, SbCycD2, SbCycB and SbCDKB were down-regulated in the repressed buds of FRtreated and defoliated seedlings indicating the suspension of cell division in those buds. However, these cell cycle-related genes were continuously expressed in the repressed buds of phyB-1, suggesting that inhibition of bud outgrowth in phyB-1 is not associated with down-regulation of cell cycle-related gene expression. The down-regulation of cell cycle-related genes in the buds of FR-treated wild type seedlings indicates that other sensors, in addition to phyB, regulate bud outgrowth in response to FR enrichment. The approaches used and results achieved will provide direction for future research on this important topic

Biomarker metabolites capturing the metabolite variance present in a rice plant developmental period

BACKGROUND: This study analyzes metabolomic data from a rice tillering (branching) developmental profile to define a set of biomarker metabolites that reliably captures the metabolite variance of this plant developmental event, and which has potential as a basis for rapid comparative screening of metabolite profiles in relation to change in development, environment, or genotype. Changes in metabolism, and in metabolite profile, occur as a part of, and in response to, developmental events. These changes are influenced by the developmental program, as well as external factors impinging on it. Many samples are needed, however, to characterize quantitative aspects of developmental variation. A biomarker metabolite set could benefit screening of quantitative plant developmental variation by providing some of the advantages of both comprehensive metabolomic studies and focused studies of particular metabolites or pathways. RESULTS: An appropriate set of biomarker metabolites to represent the plant developmental period including the initiation and early growth of rice tillering (branching) was obtained by: (1) determining principal components of the comprehensive metabolomic profile, then (2) identifying clusters of metabolites representing variation in loading on the first three principal components, and finally (3) selecting individual metabolites from these clusters that were known to be common among diverse organisms. The resultant set of 21 biomarker metabolites was reliable (P = 0.001) in capturing 83% of the metabolite variation in development. Furthermore, a subset of the biomarker metabolites was successful (P = 0.05) in correctly predicting metabolite change in response to environment as determined in another rice metabolomics study. CONCLUSION: The ability to define a set of biomarker metabolites that reliably captures the metabolite variance of a plant developmental event was established. The biomarker metabolites are all commonly present in diverse organisms, so studies of their quantitative relationships can provide comparative information concerning metabolite profiles in relation to change in plant development, environment, or genotype

Low red/far-red ratios delay spike and stem growth in wheat

The responses to low red light/far-red light (R/FR) ratios simulating dense stands were evaluated in wheat (Triticum aestivum L) cultivars released at different times in the 20th century and consequently resulting from an increasingly prolonged breeding and selection history. While tillering responses to the R/FR ratio were unaffected by the cultivars, low R/FR ratios reduced grain yield per plant (primarily grain number and secondarily grain weight per plant) particularly in modern cultivars. Low R/FR ratios delayed spike growth and development, reduced the expression of spike marker genes, accelerated the development of florets already initiated, and reduced the number of fertile florets at anthesis. It is noteworthy that low R/FR ratios did not promote stem or leaf sheath growth and therefore the observed reduction of yield cannot be accounted for as a consequence of divergence of resources towards increased plant stature. It is proposed that the regulation of yield components by the R/FR ratio could help plants to adjust to the limited availability of resources under crop conditions

Spatio-temporal land use/cover dynamics and its implication for sustainable land use in Wanka watershed, northwestern highlands of Ethiopia

Long-term land use and land cover (LULC) dynamics information is essential to understand the trends and make necessary land management interventions, such as in the highlands of Ethiopia. This study analyzed six decades of LULC dynamics of Wanka watershed, Northwestern Ethiopian highlands. Two sets of aerial photographs (1957 and 2017), SPOT 5 and sentinel satellite imageries were analyzed. In addition, key informant interviews, focus group discussions and field observations were used to identify the drivers and impact of LULC change. It was found that cultivated and rural settlement land (CRSL), bare land, and urban built up area have been continuously expanded at the expenses of mainly forest and shrub lands. Over the entire study period (1957–2017) while the bare land and CRSL have increased by about 59% and 20% respectively, forest and shrub lands have declined by 59% and 57% respectively. Urban built up area has also expanded. The impact of popula- tion pressure and expansion of CRSL land were considerable. The trend of LULC dynamics in the study watershed implies adverse impact on the quality and quantity of the land resource. Hence, appropriate land use planning and strategies that reduce expansion of cultivated land need to be practiced

Tissue tolerance: an essential but elusive trait for salt-tolerant crops

For a plant to persist in saline soil, osmotic adjustment of all plant cells is essential. The more salt-tolerant species accumulate Na+ and Cl– to concentrations in leaves and roots that are similar to the external solution, thus allowing energy-efficient osmotic adjustment. Adverse effects of Na+ and Cl– on metabolism must be avoided, resulting in a situation known as ‘tissue tolerance’. The strategy of sequestering Na+ and Cl– in vacuoles and keeping concentrations low in the cytoplasm is an important contributor to tissue tolerance. Although there are clear differences between species in the ability to accommodate these ions in their leaves, it remains unknown whether there is genetic variation in this ability within a species. This viewpoint considers the concept of tissue tolerance, and how to measure it. Four conclusions are drawn: (1) osmotic adjustment is inseparable from the trait of tissue tolerance; (2) energy-efficient osmotic adjustment should involve ions and only minimal organic solutes; (3) screening methods should focus on measuring tolerance, not injury; and (4) high-throughput protocols that avoid the need for control plants and multiple Na+ or Cl- measurements should be developed. We present guidelines to identify useful genetic variation in tissue tolerance that can be harnessed for plant breeding of salt tolerance

APETALA2 control of barley internode elongation

Many plants dramatically elongate their stems during flowering, yet how this response is coordinated with the reproductive phase is unclear. We demonstrate that microRNA (miRNA) control of APETALA2 (AP2) is required for rapid, complete elongation of stem internodes in barley, especially of the final 'peduncle' internode directly underneath the inflorescence. Disrupted miR172 targeting of AP2 in the Zeo1.b barley mutant caused lower mitotic activity, delayed growth dynamics and premature lignification in the peduncle leading to fewer and shorter cells. Stage- and tissue-specific comparative transcriptomics between Zeo1.b and its parent cultivar showed reduced expression of proliferation-associated genes, ectopic expression of maturation-related genes and persistent, elevated expression of genes associated with jasmonate and stress responses. We further show that applying methyl jasmonate (MeJA) phenocopied the stem elongation of Zeo1.b, and that Zeo1.b itself was hypersensitive to inhibition by MeJA but less responsive to promotion by gibberellin. Taken together, we propose that miR172-mediated restriction of AP2 may modulate the jasmonate pathway to facilitate gibberellin-promoted stem growth during flowering

Cereal Domestication and Evolution of Branching: Evidence for Soft Selection in the Tb1 Orthologue of Pearl Millet (Pennisetum glaucum [L.] R. Br.)

BACKGROUND: During the Neolithic revolution, early farmers altered plant development to domesticate crops. Similar traits were often selected independently in different wild species; yet the genetic basis of this parallel phenotypic evolution remains elusive. Plant architecture ranks among these target traits composing the domestication syndrome. We focused on the reduction of branching which occurred in several cereals, an adaptation known to rely on the major gene Teosinte-branched1 (Tb1) in maize. We investigate the role of the Tb1 orthologue (Pgtb1) in the domestication of pearl millet (Pennisetum glaucum), an African outcrossing cereal. METHODOLOGY/PRINCIPAL FINDINGS: Gene cloning, expression profiling, QTL mapping and molecular evolution analysis were combined in a comparative approach between pearl millet and maize. Our results in pearl millet support a role for PgTb1 in domestication despite important differences in the genetic basis of branching adaptation in that species compared to maize (e.g. weaker effects of PgTb1). Genetic maps suggest this pattern to be consistent in other cereals with reduced branching (e.g. sorghum, foxtail millet). Moreover, although the adaptive sites underlying domestication were not formerly identified, signatures of selection pointed to putative regulatory regions upstream of both Tb1 orthologues in maize and pearl millet. However, the signature of human selection in the pearl millet Tb1 is much weaker in pearl millet than in maize. CONCLUSIONS/SIGNIFICANCE: Our results suggest that some level of parallel evolution involved at least regions directly upstream of Tb1 for the domestication of pearl millet and maize. This was unanticipated given the multigenic basis of domestication traits and the divergence of wild progenitor species for over 30 million years prior to human selection. We also hypothesized that regular introgression of domestic pearl millet phenotypes by genes from the wild gene pool could explain why the selective sweep in pearl millet is softer than in maize

A Genome-Wide Association Study Identifies Variants Underlying the Arabidopsis thaliana Shade Avoidance Response

Shade avoidance is an ecologically and molecularly well-understood set of plant developmental responses that occur when the ratio of red to far-red light (R∶FR) is reduced as a result of foliar shade. Here, a genome-wide association study (GWAS) in Arabidopsis thaliana was used to identify variants underlying one of these responses: increased hypocotyl elongation. Four hypocotyl phenotypes were included in the study, including height in high R∶FR conditions (simulated sun), height in low R∶FR conditions (simulated shade), and two different indices of the response of height to low R∶FR. GWAS results showed that variation in these traits is controlled by many loci of small to moderate effect. A known PHYC variant contributing to hypocotyl height variation was identified and lists of significantly associated genes were enriched in a priori candidates, suggesting that this GWAS was capable of generating meaningful results. Using metadata such as expression data, GO terms, and other annotation, we were also able to identify variants in candidate de novo genes. Patterns of significance among our four phenotypes allowed us to categorize associations into three groups: those that affected hypocotyl height without influencing shade avoidance, those that affected shade avoidance in a height-dependent fashion, and those that exerted specific control over shade avoidance. This grouping allowed for the development of explicit hypotheses about the genetics underlying shade avoidance variation. Additionally, the response to shade did not exhibit any marked geographic distribution, suggesting that variation in low R∶FR–induced hypocotyl elongation may represent a response to local conditions