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1. Construction and comparison of three reference‐quality genome assemblies for soybean

   https://doi.org/10.1111/tpj.14500  

   Valliyodan, Babu ; Cannon, Steven B. ; Bayer, Philipp E. ; Shu, Shengqiang ; Brown, Anne V. ; Ren, Longhui ; Jenkins, Jerry ; Chung, Claire Y. ‐L. ; Chan, Ting‐Fung ; Daum, Christopher G. ; et al ( October 2019 , The Plant Journal)

   We report reference‐quality genome assemblies and annotations for two accessions of soybean (Glycine max) and for one accession ofGlycine soja, the closest wild relative ofG. max. TheG. maxassemblies provided are for widely used US cultivars: the northern line Williams 82 (Wm82) and the southern line Lee. The Wm82 assembly improves the prior published assembly, and the Lee andG. sojaassemblies are new for these accessions. Comparisons among the three accessions show generally high structural conservation, but nucleotide difference of 1.7 single‐nucleotide polymorphisms (snps) per kb between Wm82 and Lee, and 4.7 snps per kb between these lines andG. soja.snpdistributions and comparisons with genotypes of the Lee and Wm82 parents highlight patterns of introgression and haplotype structure. Comparisons against the US germplasm collection show placement of the sequenced accessions relative to global soybean diversity. Analysis of a pan‐gene collection shows generally high conservation, with variation occurring primarily in genomically clustered gene families. We found approximately 40–42 inversions per chromosome between either Lee or Wm82v4 andG. soja, and approximately 32 inversions per chromosome between Wm82 and Lee. We also investigated five domestication loci. For each locus, we found two different alleles with functional differences betweenG. sojaand the two domesticated accessions. The genome assemblies for multiple cultivated accessions and for the closest wild ancestor of soybean provides a valuable set of resources for identifying causal variants that underlie traits for the domestication and improvement of soybean, serving as a basis for future research and crop improvement efforts for this important crop species.

    

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2. A simple genetic architecture and low constraint allow rapid floral evolution in a diverse and recently radiating plant genus

   https://doi.org/10.1111/nph.15844  

   Kostyun, Jamie L. ; Gibson, Matthew J. S. ; King, Christian M. ; Moyle, Leonie C. ( May 2019 , New Phytologist)

   Genetic correlations among different components of phenotypes, especially those resulting from pleiotropy, can constrain or facilitate trait evolution. These factors could especially influence the evolution of traits that are functionally integrated, such as those comprising the flower. Indeed, pleiotropy is proposed as a main driver of repeated convergent trait transitions, including the evolution of phenotypically similar pollinator syndromes.

   We assessed the role of pleiotropy in the differentiation of floral and other reproductive traits between two species –Jaltomata sinuosaandJ. umbellata(Solanaceae) – that have divergent suites of floral traits consistent with bee and hummingbird pollination, respectively. To do so, we generated a hybrid population and examined the genetic architecture (trait segregation and quantitative trait locus (QTL) distribution) underlying 25 floral and fertility traits.

   We found that most floral traits had a relatively simple genetic basis (few, predominantly additive,QTLs of moderate to large effect), as well as little evidence of antagonistic pleiotropy (few trait correlations andQTLcolocalization, particularly between traits of different classes). However, we did detect a potential case of adaptive pleiotropy among floral size and nectar traits.

   These mechanisms may have facilitated the rapid floral trait evolution observed withinJaltomata, and may be a common component of rapid phenotypic change more broadly.

    

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3. Multivariate analysis reveals environmental and genetic determinants of element covariation in the maize grain ionome

   https://doi.org/10.1002/pld3.139  

   Fikas, Alexandra Asaro ; Dilkes, Brian P. ; Baxter, Ivan ( May 2019 , Plant Direct)

   The integrated responses of biological systems to genetic and environmental variation result in substantial covariance in multiple phenotypes. The resultant pleiotropy, environmental effects, and genotype‐by‐environmental interactions (GxE) are foundational to our understanding of biology and genetics. Yet, the treatment of correlated characters, and the identification of the genes encoding functions that generate this covariance, has lagged. As a test case for analyzing the genetic basis underlying multiple correlated traits, we analyzed maize kernel ionomes from Intermated B73 x Mo17 (IBM) recombinant inbred populations grown in 10 environments. Plants obtain elements from the soil through genetic and biochemical pathways responsive to physiological state and environment. Most perturbations affect multiple elements which leads theionome, the full complement of mineral nutrients in an organism, to vary as an integrated network rather than a set of distinct single elements. We compared quantitative trait loci (QTL) determining single‐element variation toQTLthat predict variation in principal components (PCs) of multiple‐element covariance. Single‐element and multivariate approaches detected partially overlapping sets of loci.QTLinfluencing trait covariation were detected at loci that were not found by mapping single‐element traits. Moreover, this approach permitted testing environmental components of trait covariance, and identified multi‐element traits that were determined by both genetic and environmental factors as well as genotype‐by‐environment interactions. Growth environment had a profound effect on the elemental profiles and multi‐element phenotypes were significantly correlated with specific environmental variables.

    

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4. Direct and indirect selection on flowering time, water‐use efficiency ( WUE , δ 13 C), and WUE plasticity to drought in Arabidopsis thaliana

   https://doi.org/10.1002/ece3.1270  

   Kenney, Amanda M. ; McKay, John K. ; Richards, James H. ; Juenger, Thomas E. ( November 2014 , Ecology and Evolution)

   Flowering time and water‐use efficiency (WUE) are two ecological traits that are important for plant drought response. To understand the evolutionary significance of natural genetic variation in flowering time,WUE, andWUEplasticity to drought inArabidopsis thaliana, we addressed the following questions: (1) How are ecophysiological traits genetically correlated within and between different soil moisture environments? (2) Does terminal drought select for early flowering and drought escape? (3) IsWUEplasticity to drought adaptive and/or costly? We measured a suite of ecophysiological and reproductive traits on 234 spring flowering accessions ofA. thalianagrown in well‐watered and season‐ending soil drying treatments, and quantified patterns of genetic variation, correlation, and selection within each treatment.WUEand flowering time were consistently positively genetically correlated.WUEwas correlated withWUEplasticity, but the direction changed between treatments. Selection generally favored early flowering and lowWUE, with drought favoring earlier flowering significantly more than well‐watered conditions. Selection for lowerWUEwas marginally stronger under drought. There were no net fitness costs ofWUEplasticity.WUEplasticity (per se) was globally neutral, but locally favored under drought. Strong genetic correlation betweenWUEand flowering time may facilitate the evolution of drought escape, or constrain independent evolution of these traits. Terminal drought favored drought escape in these spring flowering accessions ofA. thaliana.WUEplasticity may be favored over completely fixed development in environments with periodic drought.

    

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5. Cultivated sunflower ( Helianthus annuus L.) has lower tolerance of moderate drought stress than its con‐specific wild relative, but the underlying traits remain elusive

   https://doi.org/10.1002/pld3.581  

   Tran, Vivian H. ; Nolting, Kristen M. ; Donovan, Lisa A. ; Temme, Andries A. ( April 2024 , Plant Direct)

   Cultivated crops are generally expected to have less abiotic stress tolerance than their wild relatives. However, this assumption is not well supported by empirical literature and may depend on the type of stress and how it is imposed, as well as the measure of tolerance being used. Here, we investigated whether wild and cultivated accessions ofHelianthus annuusdiffered in stress tolerance assessed as proportional decline in biomass due to drought and whether wild and cultivated accessions differed in trait responses to drought and trait associations with tolerance. In a greenhouse study,H. annuusaccessions in the two domestication classes (eight cultivated and eight wild accessions) received two treatments: a well‐watered control and a moderate drought implemented as a dry down followed by maintenance at a predetermined soil moisture level with automated irrigation. Treatments were imposed at the seedling stage, and plants were harvested after 2 weeks of treatment. The proportional biomass decline in response to drought was 24% for cultivatedH. annuusaccessions but was not significant for the wild accessions. Thus, using the metric of proportional biomass decline, the cultivated accessions had less drought tolerance. Among accessions, there was no tradeoff between drought tolerance and vigor assessed as biomass in the control treatment. In a multivariate analysis, wild and cultivated accessions did not differ from each other or in response to drought for a subset of morphological, physiological, and allocational traits. Analyzed individually, traits varied in response to drought in wild and/or cultivated accessions, including declines in specific leaf area, leaf theoretical maximum stomatal conductance (g_smax), and stomatal pore length, but there was no treatment response for stomatal density, succulence, or the ability to osmotically adjust. Focusing on traits associations with tolerance, plasticity in g_smaxwas the most interesting because its association with tolerance differed by domestication class (although the effects were relatively weak) and thus might contribute to lower tolerance of cultivated sunflower. OurH. annuusresults support the expectation that stress tolerance is lower in crops than wild relatives under some conditions. However, determining the key traits that underpin differences in moderate drought tolerance between wild and cultivatedH. annuusremains elusive.

    

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