We report reference‐quality genome assemblies and annotations for two accessions of soybean (
To clarify the molecular bases of flowering time evolution in crop domestication, here we investigate the evolutionary fates of a set of four recently duplicated genes in soybean:
- NSF-PAR ID:
- 10034341
- Publisher / Repository:
- Wiley-Blackwell
- Date Published:
- Journal Name:
- The Plant Journal
- Volume:
- 90
- Issue:
- 5
- ISSN:
- 0960-7412
- Page Range / eLocation ID:
- p. 941-953
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
More Like this
-
Summary Glycine max ) and for one accession ofGlycine soja , the closest wild relative ofG. max . TheG. max assemblies 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. soja assemblies are new for these accessions. Comparisons among the three accessions show generally high structural conservation, but nucleotide difference of 1.7 single‐nucleotide polymorphisms (snp s) per kb between Wm82 and Lee, and 4.7snp s per kb between these lines andG. soja .snp distributions 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. soja and 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. -
Abstract 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 , andWUE plasticity 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) IsWUE plasticity to drought adaptive and/or costly? We measured a suite of ecophysiological and reproductive traits on 234 spring flowering accessions ofA. thaliana grown in well‐watered and season‐ending soil drying treatments, and quantified patterns of genetic variation, correlation, and selection within each treatment.WUE and flowering time were consistently positively genetically correlated.WUE was correlated withWUE plasticity, 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 lowerWUE was marginally stronger under drought. There were no net fitness costs ofWUE plasticity.WUE plasticity (per se) was globally neutral, but locally favored under drought. Strong genetic correlation betweenWUE and 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 .WUE plasticity may be favored over completely fixed development in environments with periodic drought. -
Abstract Brassinosteroids (
BRs ) are essential plant growth‐promoting hormones involved in many processes throughout plant development, from seed germination to flowering time. SinceBRs do not undergo long‐distance transport, cell‐ and tissue‐specific regulation of hormone levels involves both biosynthesis and inactivation. To date, tenBR ‐inactivating enzymes, with at least five distinct biochemical activities, have been experimentally identified in the model plantArabidopsis thaliana . Epigenetic interactions betweenT‐DNA insertion alleles and genetic linkage have hindered analysis of higher‐order null mutants in these genes. A previous study demonstrated that thebas1‐2 sob7‐1 ben1‐1 triple‐null mutant could not be characterized due to epigenetic interactions between the exonicT‐DNA insertions inbas1‐2 andsob7‐1, causing the intronicT‐DNA insertion ofben1‐1 to revert to a partial loss‐of‐function allele. We usedCRISPR‐Cas9 genome editing to avoid this problem and generated thebas1‐2 sob7‐1 ben1‐3 triple‐null mutant. This triple‐null mutant resulted in an additive seedling long‐hypocotyl phenotype. We also uncovered a role for ‐mediatedBEN1 BR ‐inactivation in seedling cotyledon petiole elongation that was not observed in the singleben1‐2 null mutant but only in the absence of both andBAS1 . In addition, genetic analysis demonstrated thatSOB7 does not contribute to the early‐flowering phenotype, whichBEN1 andBAS1 redundantly regulate. Our results show thatSOB7 ,BAS1 andBEN1 , have overlapping and independent roles based on their differential spatiotemporal tissue expression patternsSOB7 -
Convergent evolution of root system architecture in two independently evolved lineages of weedy rice
Summary Root system architecture (
RSA ) is a critical aspect of plant growth and competitive ability. Here we used two independently evolved strains of weedy rice, a de‐domesticated form of rice, to study the evolution of weed‐associatedRSA traits and the extent to which they evolve through shared or different genetic mechanisms.We characterised 98 two‐dimensional and three‐dimensional
RSA traits in 671 plants representing parents and descendants of two recombinant inbred line populations derived from two weed × crop crosses. A random forest machine learning model was used to assess the degree to which root traits can predict genotype and the most diagnostic traits for doing so. We used quantitative trait locus (QTL) mapping to compare genetic architecture between the weed strains.The two weeds were distinguishable from the crop in similar and predictable ways, suggesting independent evolution of a ‘weedy’
RSA phenotype. Notably, comparativeQTL mapping revealed little evidence for shared underlying genetic mechanisms.Our findings suggest that despite the double bottlenecks of domestication and de‐domestication, weedy rice nonetheless shows genetic flexibility in the repeated evolution of weedy
RSA traits. Whereas the root growth of cultivated rice may facilitate interactions among neighbouring plants, the weedy rice phenotype may minimise below‐ground contact as a competitive strategy. -
Summary Many plants require prolonged exposure to cold to acquire the competence to flower. The process by which cold exposure results in competence is known as vernalization. In
Arabidopsis thaliana , vernalization leads to the stable repression of the floral repressor via chromatin modification, including an increase of trimethylation on lysine 27 of histone H3 (H3K27me3) by Polycomb Repressive Complex 2 (FLOWERING LOCUS CPRC 2). Vernalization in pooids is associated with the stable induction of a floral promoter, (VERNALIZATION 1VRN1 ). From a screen for mutants with a reduced vernalization requirement in the model grassBrachypodium distachyon , we identified two recessive alleles of (ENHANCER OF ZESTE ‐LIKE 1 ).EZL 1 is orthologous toEZL 1A. thaliana , a gene that encodes the catalytic subunit ofCURLY LEAF 1PRC 2.B. distachyon ezl1 mutants flower rapidly without vernalization in long‐day (LD ) photoperiods; thus, is required for the proper maintenance of the vegetative state prior to vernalization. Transcriptomic studies inEZL 1ezl1 revealed mis‐regulation of thousands of genes, including ectopic expression of several floral homeotic genes in leaves. Loss of results in the global reduction of H3K27me3 and H3K27me2, consistent with this gene making a major contribution toEZL 1PRC 2 activity inB. distachyon . Furthermore, inezl1 mutants, the flowering genes andVRN 1 (AGAMOUS ) are ectopically expressed and have reduced H3K27me3. Artificial microAG RNA knock‐down of either orVRN 1 inAG ezl1‐1 mutants partially restores wild‐type flowering behavior in non‐vernalized plants, suggesting that ectopic expression inezl1 mutants may contribute to the rapid‐flowering phenotype.