Novel and Transgressive Salinity Tolerance in Recombinant Inbred Lines of Rice Created by Physiological Coupling-Uncoupling and Network Rewiring Effects.

The phenomenon of transgressive segregation, where a small minority of recombinants are outliers relative to the range of parental phenotypes, is commonly observed in plant breeding populations. While this phenomenon has been attributed to complementation and epistatic effects, the physiological and developmental synergism involved have not been fully illuminated by the QTL mapping approach alone, especially for stress-adaptive traits involving highly complex interactions. By systems-level profiling of the IR29 × Pokkali recombinant inbred population of rice, we addressed the hypothesis that novel salinity tolerance phenotypes are created by reconfigured physiological networks due to positive or negative coupling-uncoupling of developmental and physiological attributes of each parent. Real-time growth and hyperspectral profiling distinguished the transgressive individuals in terms of stress penalty to growth. Non-parental network signatures that led to either optimal or non-optimal integration of developmental with stress-related mechanisms were evident at the macro-physiological, biochemical, metabolic, and transcriptomic levels. Large positive net gain in super-tolerant progeny was due to ideal complementation of beneficial traits while shedding antagonistic traits. Super-sensitivity was explained by the stacking of multiple antagonistic traits and loss of major beneficial traits. The synergism uncovered by the phenomics approach in this study supports the modern views of the Omnigenic Theory, emphasizing the synergy or lack thereof between core and peripheral components. This study also supports a breeding paradigm rooted on genomic modeling from multi-dimensional genetic, physiological, and phenotypic profiles to create novel adaptive traits for new crop varieties of the 21st century.

Networks of Physiological Adjustments and Defenses, and Their Synergy With Sodium (Na+) Homeostasis Explain the Hidden Variation for Salinity Tolerance Across the Cultivated Gossypium hirsutum Germplasm.

The abilities to mobilize and/or sequester excess ions within and outside the plant cell are important components of salt-tolerance mechanisms. Mobilization and sequestration of Na+ involves three transport systems facilitated by the plasma membrane H+/Na+ antiporter (SOS1), vacuolar H+/Na+ antiporter (NHX1), and Na+/K+ transporter in vascular tissues (HKT1). Many of these mechanisms are conserved across the plant kingdom. While Gossypium hirsutum (upland cotton) is significantly more salt-tolerant relative to other crops, the critical factors contributing to the phenotypic variation hidden across the germplasm have not been fully unraveled. In this study, the spatio-temporal patterns of Na+ accumulation along with other physiological and biochemical interactions were investigated at different severities of salinity across a meaningful genetic diversity panel across cultivated upland Gossypium. The aim was to define the importance of holistic or integrated effects relative to the direct effects of Na+ homeostasis mechanisms mediated by GhHKT1, GhSOS1, and GhNHX1. Multi-dimensional physio-morphometric attributes were investigated in a systems-level context using univariate and multivariate statistics, randomForest, and path analysis. Results showed that mobilized or sequestered Na+ contributes significantly to the baseline tolerance mechanisms. However, the observed variance in overall tolerance potential across a meaningful diversity panel were more significantly attributed to antioxidant capacity, maintenance of stomatal conductance, chlorophyll content, and divalent cation (Mg2+) contents other than Ca2+ through a complex interaction with Na+ homeostasis. The multi-tier macro-physiological, biochemical and molecular data generated in this study, and the networks of interactions uncovered strongly suggest that a complex physiological and biochemical synergy beyond the first-line-of defense (Na+ sequestration and mobilization) accounts for the total phenotypic variance across the primary germplasm of Gossypium hirsutum. These findings are consistent with the recently proposed Omnigenic Theory for quantitative traits and should contribute to a modern look at phenotypic selection for salt tolerance in cotton breeding.

Understanding diploid diversity: A first step in unraveling polyploid, apomictic complexity in Amelanchier.

PREMISE OF THE STUDY: Delimitation of Amelanchier species is difficult because of polyploidy and gametophytic apomixis. A first step in unraveling this species problem is understanding the diversity of the diploids that contributed genomes to polyploid apomicts. This research helps clarify challenging species-delimitation problems attending polyploid, apomictic complexity. METHODS: We sampled 431 diploid accessions from 13 species, of which 10 are North American and three are Old World. Quantitative morphological analyses tested the null hypothesis of no discrete groups. Using three to nine diploid accessions per species, we constructed phylogenies with DNA sequences from ETS, ITS, the second intron of LEAFY, and chloroplast regions rpoB-trnC, rpl16, trnD-trnT, and ycf6-psbM. KEY RESULTS: Most Amelanchier diploid taxa are morphologically and ecogeographically distinct and genetically exclusive lineages. They rarely hybridize with one another. Nuclear and chloroplast DNA sequences almost completely resolve the Amelanchier phylogeny. The backbone is the mostly western North American clade A, eastern North American clade B, and Old World clade O. DNA sequences and morphology support clades A and O as sister taxa. Despite extensive paralogy, our LEAFY data are phylogenetically informative and identify a clade (T) of three arborescent taxa within clade B. CONCLUSIONS: Amelanchier diploids differ strikingly from polyploid apomicts, in that hybridization among them is rare, and they form taxa that would qualify as species by most species concepts. Knowledge of diploid morphology, phylogeny, and ecogeography provides a foundation for understanding the evolutionary history of polyploid apomicts, their patterns of diversification, and their species status.

Effects of apomixis and polyploidy on diversification and geographic distribution in Amelanchier (Rosaceae).

UNLABELLED: • PREMISE OF THE STUDY: Amelanchier polyploid apomicts differ from sexual diploids in their more complex diversification, greater species problems, and geographic distribution. To understand these differences, we investigated the occurrence of polyploidy and frequency of apomixis. This research helps clarify species delimitation in an evolutionarily complex genus.• METHODS: We used flow cytometry to estimate genome size of 1355 plants. We estimated the frequency of apomixis from flow-cytometrically determined ploidy levels of embryo and endosperm and from a progeny study using RAPD markers. We explored relationships of triploids to other ploidy levels and of ploidy levels to latitude plus elevation.• KEY RESULTS: Diploids (32% of sample) and tetraploids (62%) were widespread. Triploids (6%) mostly occurred in small numbers with diploids from two or more species or with diploids and tetraploids. Seeds from diploids were 2% apomictic, the first report of apomixis in Amelanchier diploids. Seeds from triploids were 75% apomictic. We documented potential triploid bridge and triploid block from unbalanced endosperm and low pollen viability. Seeds from tetraploids were 97% apomictic, and tetraploids often formed microspecies. We did not find strong evidence for geographical parthenogenesis in North American Amelanchier. Most currently recognized species contained multiple ploidy levels that were morphologically semicryptic.• CONCLUSIONS: Documentation of numerous transitions from diploidy to polyploidy helps clarify diversification, geographic distribution, and the species problem in Amelanchier. Despite the infrequent occurrence of triploids, their retention of 25% sexuality and capacity for triploid bridge may be important steps between sexual diploids and predominantly apomictic tetraploids.