The inherent complexity of adaptive mechanisms to salinity stress necessitates novel approaches to plant breeding. In rice, wide introgression is an approach that is yet to be fully exploited, especially from the not-so-distant species related to cultivars. We explored the genetic combining potential of the AA-genome wild species Oryza rufipogon, the closest progenitor of cultivated Oryza sativa ssp. japonica, to uncover physiological novelties for salinity tolerance created by transgressive effects. Comprehensive evaluation of a set of chromosome segment substitution lines (CSSL) for various physiometric traits revealed the occurrence of individuals transgressing the parental phenotypic range. This indicates that introgression of alien O. rufipogon genomic segments into O. sativa genomic background can alter the overall potential of the recipient by creating novel physiological attributes better than the donor or worse than the recipient. In-depth characterization of transgressive tolerant and transgressive sensitive CSSLs showed the occurrence of novel attributes in terms of energy balance and gas exchange that positively correlated with enhanced or reduced potential for salinity tolerance. Integrated morphological, physiological, biochemical, ionomic, genomic, and transcriptomic profiling revealed five genomic regions with QTL effects, and seven genes with putative eQTL effects that explain the occurrence of transgressive phenotypes. Genes with eQTL effects are associated with the regulation of cytokinin-mediated processes, MYB transcription factors, and transmembrane transport, that positively correlated with the maintenance of shoot biomass, regulation of stomatal conductance, and modulation of cellular homeostasis. The transgressive lines had non-parental expression patterns for eleven genes that originated from O. rufipogon. These genes gained new patterns of regulation (de-regulation effects) in the genomic background of O. sativa indicating the unleashing of cryptic functions through introgression.

Dhurrin is a cyanogenic glucoside found in all vegetative tissues of Sorghum bicolor, functioning as a herbivore repellent, antifungal agent, osmoprotectant, and nitrogen (N) storage. Dhurrin concentration is usually highest in young seedlings, where it rapidly accumulates following germination, after which its biosynthesis decreases and its turnover increases as the seedling ages. To avoid prussic acid poisoning from dhurrin catabolism in cattle grazing or foraging on sorghum, numerous research studies now focus on breeding for dhurrin-free or acyanogenic sorghum using EMS (Ethyl methanesulfonate) mutants with a non-functional dhurrin biosynthetic pathway. However, there has been limited and conflicting research investigating the role dhurrin plays as a potential nitrogen source in sorghum’s early seedling growth, especially under N deficiency. It is plausible that the presence of background mutations in dhurrin-free sorghum mutants could mask or confound how the absence of dhurrin affects early seedling growth. Using a naturally occurring (non-mutant) ultra-low dhurrin genotype and known low and high dhurrin genotypes, the current research investigated the importance of dhurrin as a potential endogenous nitrogen source for early seedling growth in simulated non-marginal (N-available) and marginal (N-deficient) media. Dhurrin was implicated to be an N source for seedling growth from 8 to 13 days after planting under deficient N conditions. In N-deficient media at 13 days after planting, high-dhurrin-level genotypes accumulated more seedling fresh shoot biomass than low-dhurrin-level genotypes. Thus, while acyanogenic sorghum will be beneficial in expanding sorghum’s economic value, the use of dhurrin knock-out mutants can prove problematic since the complete lack of dhurrin may affect field germination and stand establishment, particularly under N-deficient or low-N-input conditions.

IntroductionElevated atmospheric carbon dioxide [CO2] increases peanut carbon assimilation and productivity. However, the molecular basis of such responses is not well understood. We tested the hypothesis that maintaining high photosynthesis under long-term elevated [CO2] is associated with the shift in C metabolism gene expression regulation.MethodsWe used a field CO2 enrichment system to examine the effects of elevated [CO2] (ambient + 250 ppm) across different soil water availability and plant developmental stages on the molecular responses in a peanut runner-type genotype. Plants under both [CO2] treatments were grown in semiarid conditions. We evaluated a comparative leaf transcriptomic profile across three periodic water deficit/re-hydration (well-watered/recovery) cycles throughout the growing season using RNAseq analysis.ResultsOur results showed that the transcriptome responses were influenced by [CO2], water availability, and developmental stages. The traditional Mercator annotation analysis based on percentage total revealed that lipid metabolism, hormone biosynthesis, secondary metabolism, amino acid biosynthesis, and transport were the most regulated biological processes. However, our new approach based on the comparative relative percentage change per individual category across stages revealed new insights into the gene expression patterns of biological functional groups, highlighting the relevance of the C-related pathways regulated by elevated [CO2].DiscussionThe photosynthesis analysis showed that 1) The light reaction was the most upregulated pathway by elevated [CO2] during water stress, 2) Photorespiration was downregulated across all stages, 3) Sucrose synthesis genes were upregulated by elevated [CO2] before stress, 4) Starch synthesis genes were upregulated by elevated [CO2] under drought periods, and 5) CO2 regulation of sucrose and starch degradation was critical under drought periods. Our findings provide valuable insights into the molecular basis underlying the photosynthetic acclimation response to elevated [CO2] in peanuts.

AbstractIncreasing crop production in a changing climate is one of the challenges facing the agricultural research community. The goal of this study was to identify and evaluate specific determinant traits for improving water stress resiliency of cultivated upland cotton (Gossypium hirsutum L.). Two genotypes (PhytoGen 72 [PHY72] and Stoneville 474 [STV474]) representing different production regions of the US were evaluated for water stress resiliency under greenhouse conditions. More than 20 vegetative and reproductive traits were evaluated through six physiological reproductive stages, from plant emergence to open bolls and under two irrigation levels. Significant differences (p ≤ 0.05) were observed between irrigation levels for most traits within each genotype. PHY72 had rapid increases in plant height under regular water and limited water conditions (RW and LW). RW approximated daily evapotranspiration rates, while LW rate provided 50% less water by mass. However, by the fourth stage, peak blooming, the two genotypes were the same height, indicating that early and rapid vegetative plant growth from emergence to first reproductive stage was not a good indicator of improved growth and boll production under diverse irrigation levels. Some traits, such as leaf temperature, chlorophyll fluorescence yield, leaf and boll number, as well as leaf and reproductive fresh weight, showed clear differences between the two genotypes in one or both irrigation rates. Cotton breeders/geneticists currently cannot predict end‐of‐season productivity based on early‐season evaluations under water stress conditions. Early season, controlled environment screening before field testing may reveal the genetic potential of breeding lines for water stress resiliency.

A wealth of quantitative trait loci and candidate genes that were, respectively, found linked to or associated with phenotypic traits of interest has accumulated in sorghum [Sorghum bicolor (L.) Moench] from myriad genetic mapping projects. Since sorghum's first quality reference genome was delivered in 2009, many mapping populations have been developed or assembled to successfully identify an estimated 660 marker-trait associations (MTAs) to narrow down genomic regions that individually harbor putative genes, which fluctuates tremendously based on regional linkage disequilibrium and gene density. Only some 8% of studies have validated the causal genes, much less the functional alleles, underlying these regions or candidate genes of interest, despite the resources now available to do so. This chapter focuses on the success stories in sorghum that have identified functional alleles for major effect genes, but also details the opportunities that exist for allele mining in the era of publicly available sorghum pangenomes and genomic database resources.

The BTB/POZ family of proteins is widespread in plants and animals, playing important roles in development, growth, metabolism, and environmental responses. Although members of the expanded BTB/POZ gene family (OsBTB) have been identified in cultivated rice (Oryza sativa), their conservation, novelty, and potential applications for allele mining in O. rufipogon, the direct progenitor of O. sativa ssp. japonica and potential wide-introgression donor, are yet to be explored. This study describes an analysis of 110 BTB/POZ encoding gene loci (OrBTB) across the genome of O. rufipogon as outcomes of tandem duplication events. Phylogenetic grouping of duplicated OrBTB genes was supported by the analysis of gene sequences and protein domain architecture, shedding some light on their evolution and functional divergence. The O. rufipogon genome encodes nine novel BTB/POZ genes with orthologs in its distant cousins in the family Poaceae (Sorghum bicolor, Brachypodium distachyon), but such orthologs appeared to have been lost in its domesticated descendant, O. sativa ssp. japonica. Comparative sequence analysis and structure comparisons of novel OrBTB genes revealed that diverged upstream regulatory sequences and regulon restructuring are the key features of the evolution of this large gene family. Novel genes from the wild progenitor serve as a reservoir of potential new alleles that can bring novel functions to cultivars when introgressed by wide hybridization. This study establishes a foundation for hypothesis-driven functional genomic studies and their applications for widening the genetic base of rice cultivars through the introgression of novel genes or alleles from the exotic gene pool.

AbstractThe BTB/POZ family of proteins is widespread in plants and animals, playing important roles in development, growth, metabolism, and environmental responses. Although members of the expanded BTB/POZ gene family (OsBTB) have been identified in cultivated rice (Oryza sativa), their conservation, novelty, and potential applications for allele mining inO. rufipogon, the direct progenitor ofO. sativassp. japonica and potential wide-introgression donor, are yet to be explored. This study describes an analysis of 110 BTB/POZ encoding gene loci (OrBTB) across the genome ofO. rufipogonas outcomes of tandem duplication events. Phylogenetic grouping of duplicatedOrBTBgenes was supported by the analysis of gene sequences and protein domain architecture, shedding some light on their evolution and functional divergence. TheO. rufipogongenome encodes eight novel BTB/POZ genes with orthologs in its distant cousins in the family Poaceae (Sorghum bicolor, Brachypodium distachyon), but such orthologs appeared to have been lost in its domesticated descendant,O. sativassp. japonica. Comparative sequence analysis and structure comparisons of novelOrBTBgenes revealed that diverged upstream regulatory sequences and regulon restructuring are the key features of the evolution of this large gene family. Novel genes from the wild progenitor serve as a reservoir of potential new alleles that can bring novel functions to cultivars when introgressed by wide hybridization. This study establishes a foundation for hypothesis-driven functional genomic studies and their applications for widening the genetic base of rice cultivars through the introgression of novel genes or alleles from the exotic gene pool.

Trabajo presentado en el XII Conference of the Iberian Association for Comparative Endocrinology (AIEC), celebrado en Faro (Portugal), del 26 al 28 de septiembre de 2019

Introgression of major-effect QTLs is an important component of rice breeding for yield-retention under drought. While largely effective, the maximum potentials of such QTLs have not been consistent across genetic backgrounds. We hypothesized that synergism or antagonism with additive-effect peripheral genes across the background could either enhance or undermine the QTL effects. To elucidate the molecular underpinnings of such interaction, we dissected qDTY12.1 synergy with numerous peripheral genes in context of network rewiring effects. By integrative transcriptome profiling and network modeling, we identified the DECUSSATE ( OsDEC ) within qDTY12.1 as the core of the synergy and shared by two sibling introgression lines in IR64 genetic background, i.e., LPB (low-yield penalty) and HPB (high-yield penalty). OsDEC is expressed in flag leaves and induced by progressive drought at booting stage in LPB but not in HPB. The unique OsDEC signature in LPB is coordinated with 35 upstream and downstream peripheral genes involved in floral development through the cytokinin signaling pathway, which are lacking in HPB. Results further support the differential network rewiring effects through genetic coupling-uncoupling between qDTY12.1 and other upstream and downstream peripheral genes across the distinct genetic backgrounds of LPB and HPB. We propose that the functional DEC -network in LPB defines a mechanism for early flowering as a means for avoiding the depletion of photosyntate needed for reproductive growth due to drought. Its impact on yield-retention is likely through the timely establishment of stronger source-sink dynamics that sustains a robust reproductive transition under drought. Author summary While the Green Revolution of the 1960’s significantly increased rice grain yields through the creation of high-yielding varieties for high input systems, current marginal climates pose a significant challenge for providing consistent yield. In rice growing regions of the world, drought affects the livelihood of small-scale and subsistence farmers by inflicting significant yield penalties to their production systems. Breeding of next-generation rice varieties with optimal balance of survivability and productivity traits will be key to providing consistent yields year to year. Within this paradigm, the use of large effect QTLs such as qDTY12.1 to improve yield retention under drought have been largely successful. By integrating the use of high resolution transcriptome datasets with a focused biological interrogation of agronomic results from this and previous studies, we uncovered a putative functional genetic network, anchored by the DECUSSATE gene ( OsDEC ) within qDTY12.1 , that effectively minimizes drought penalties to yield by driving cellular processes that culminate in timely flowering that maximizes the use of photosynthetic sources for efficient reproduductive transition and ultimately seed development. Our study further illuminates the qDTY12.1 function and speaks to the misconception that qDTY introgression alone is sufficient for providing consistently large positive effects to yield retention under reproductive stage drought.

Early planted sorghum usually experiences cooler day/night temperatures, which may result in delayed growth, floral initiation, and infertile pollen, limiting productivity in high altitudes and temperate regions. Genetic variability for cold tolerance in sorghum has been evaluated by characterizing germination, emergence, vigor, and seedling growth under sub-optimal temperatures. However, the compounded effect of early season cold on plant growth and development and subsequent variability in potential grain yield losses has not been evaluated. Agro-morphological and physiological responses of sorghum grown under early-, mid-, and standard planting dates in West Texas were characterized from seed-to-seed. A set of diverse lines and hybrids with two major sources of tolerance, and previously selected for seedling cold tolerance were used. These were evaluated with a standard commercial hybrid known for its seedling cold tolerance and some cold susceptible breeding lines as checks. Variabilities in assessed parameters at seedling, early vegetative, and maturity stages were observed across planting dates for genotypes and sources of cold tolerance. Panicle initiation was delayed, and panicle size reduced, resulting in decreased grain yields under early and mid-planting dates. Coupled with final germination percent, panicle width and area were significant unique predictors of yield under early and mid-planting dates. Significant variability in performance was observed not only between cold tolerant and susceptible checks, but noticeably between sources of cold tolerance, with the Ethiopian highland sources having lesser yield penalties than their Chinese counterparts. Thus, screening for cold tolerance should not be limited to early seedling characterization but should also consider agronomic traits that may affect yield penalties depending on the sources of tolerance.

Silverleaf nightshade (Solanum elaeagnifolium Cav.) is a noxious weed that threatens agricultural productivity and biodiversity worldwide. The long-term management of soil seedbanks along with the aboveground populations of silverleaf nightshade has the potential to effectively control the species in its introduced range. Implementation of this strategy requires insights into the germination behavior of the weed in response to various environmental stimuli and endogenous cues. We assessed the morphology and germination of silverleaf nightshade seeds from an agricultural farm, native rangelands, and an urban site in Texas, USA. The effects of growth substrate, phytohormones, and salt treatments on seed germination were also evaluated to identify potential stimulus that can be used to manipulate germination in the species. Results of the study showed that silverleaf nightshade seeds from the agricultural farm were the largest, while those from the Littlefield rangeland were the smallest. Seeds collected from the urban site and agricultural farm have higher germination rates than those sampled from the rangelands. Compared to domesticated crops, silverleaf nightshade seeds require longer imbibition time. Seed germination was better in potting mix than in sand or combined potting mix and sand and was significantly reduced by salt and abscisic acid treatments. Overall, results of the study highlight the crucial role of local environments in conditioning the transgenerational adaptation of species, particularly with respect to germination. Recommendations for silverleaf nightshade control are presented based on the observed variations in the germination behavior of populations within specific ranges.

The impact of qDTY12.1 in maintaining yield under drought has not been consistent across genetic backgrounds. We hypothesized that synergism or antagonism with additive-effect peripheral genes across the background genome either enhances or undermines its full potential. By modeling the transcriptional networks across sibling qDTY12.1-introgression lines with contrasting yield under drought (LPB = low-yield penalty; HPB = high-yield penalty), the qDTY12.1-encoded DECUSSATE gene (OsDEC) was revealed as the core of a synergy with other genes in the genetic background. OsDEC is expressed in flag leaves and induced by progressive drought at booting stage in LPB but not in HPB. The unique OsDEC signature in LPB is coordinated with 35 upstream and downstream peripheral genes involved in floral development through the cytokinin signaling pathway. Results support the differential network rewiring effects through genetic coupling-uncoupling between qDTY12.1 and other upstream and downstream peripheral genes across the distinct genetic backgrounds of LPB and HPB. The functional DEC-network in LPB defines a mechanism for early flowering as a means for avoiding the drought-induced depletion of photosynthate needed for reproductive growth. Its impact is likely through the timely establishment of stronger source-sink dynamics that sustains a robust reproductive transition under drought.

Cotton is widely cultivated in temperate regions across the world and is often constrained by a short planting window that is bookended by low, suboptimal temperatures. With the growing interest in early season planting, improvements in the cold germination ability of cotton will be necessary to ensure the production stability of early planted crops. The importance of saturation levels of membrane and storage lipids in enhancing cold tolerance in plants, as well as improving cold germination ability in seeds have been widely researched in a range of plant species. While studies have shown that higher levels of unsaturated lipids can enhance cold germination ability and reduce seedling injury in other crops, similar efforts have been fairly limited in cotton. This review looks at the functional properties of membrane and storage lipids, and their role in membrane stability and reorganization during the early stages of germination. Additionally, the importance of storage lipid composition as an energy source to the growing embryo is described in the context of cellular energetics (i.e., fatty acid catabolism). Finally, perspectives in improving the cold germination of upland cotton by manipulating the fatty acid composition of both membrane and storage lipid content of seeds are presented.