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Summary: Tiller number per plant—a cardinal component of ideal plant architecture—affects grain yield potential. Thus, alleles positively affecting tillering must be mined to promote genetic improvement. Here, we report a Tiller Number 1 (TN1) protein harbouring a bromo‐adjacent homology domain and RNA recognition motifs, identified through genome‐wide association study of tiller numbers. Natural variation in TN1 affects its interaction with TIF1 (TN1 interaction factor 1) to affect DWARF14 expression and negatively regulate tiller number in rice. Further analysis of variations in TN1 among indica genotypes according to geographical distribution revealed that low‐tillering varieties with TN1‐hapL are concentrated in Southeast Asia and East Asia, whereas high‐tillering varieties with TN1‐hapH are concentrated in South Asia. Taken together, these results indicate that TN1 is a tillering regulatory factor whose alleles present apparent preferential utilization across geographical regions. Our findings advance the molecular understanding of tiller development. [ABSTRACT FROM AUTHOR]

[Display omitted] • We quantified the genome wide consequences of selection responsible for the subspecific and population differentiation of rice before and during domestication using a 3D differentiation model, which provided insights into the evolutionary process of rice. • We showed the presence of equivalent rich genomic diversity and subspecific/population differentiation within both Os (landraces) and Or of the similar geographic origins and sample sizes, providing strong evidence rejecting the single origin (domestication) model of Os from China. • Our results revealed the evolutionary dynamics of rice at the genomic level during domestication and modern breeding by comparing the genome wide selective signatures. • Our results, combined with all available evidence from previous studies, led us to a new hypothesis of multiple independent domestications of Os at different sites and timing over a long period of time in Asia with the earliest domestication events occurred in China. • Our results suggest the more efficient utilization of the rich diversity within Os by exploiting inter-subspecific and among population diversity in future rice improvement. Rice, Oryza sativa L. (Os), is one of the oldest domesticated cereals that has also gone through extensive improvement in modern breeding. How rice was domesticated and impacted by modern breeding. We performed comprehensive analyses of genomic sequences of 504 accessions of Os and 456 accessions of O. rufipogon/O. nivara (Or). The natural selection on Or before domestication and the natural and artificial selection during domestication together shaped the well-differentiated genomes of two subspecies, geng(j) (japonica) and xian(i) (indica), while breeding has made apparent genomic imprints between landrace and modern varieties of each subspecies, and also between primary modern and advanced modern varieties of xian(i). Selection during domestication and breeding left genome-wide selective signals covering ∼ 22.8 % and ∼ 8.6 % of the Os genome, significantly reduced within-population genomic diversity by ∼ 22 % in xian(i) and ∼ 53 % in geng(j) plus more pronounced subspecific differentiation. Only ∼ 10 % reduction in the total genomic diversity was observed between the Os and Or populations, indicating domestication did not suffer severe genetic bottleneck. Our results revealed clear differentiation of the Or accessions into three large populations, two of which correspond to the well-differentiated Os subspecies, geng(j) and xian(i). Improved productivity and common changes in the same suit of adaptive traits in xian(i) and geng(j) during domestication and breeding resulted apparently from compensatory and convergent selections for different genes/alleles acting in the common KEGG terms and/or same gene families, and thus maintaining or even increasing the within population diversity and subspecific differentiation of Os, while more genes/alleles of novel function were selected during domestication than modern breeding. Our results supported the multiple independent domestication of Os in Asia and suggest the more efficient utilization of the rich diversity within Os by exploiting inter-subspecific and among population diversity in future rice improvement. [ABSTRACT FROM AUTHOR]

Summary: Yield in rice is determined mainly by panicle architecture. Using map‐based cloning, we identified an R2R3 MYB transcription factor REGULATOR OF GRAIN NUMBER1 (RGN1) affecting grain number and panicle architecture. Mutation of RGN1 caused an absence of lateral grains on secondary branches. We demonstrated that RGN1 controls lateral grain formation by regulation of LONELY GUY (LOG) expression, thus controlling grain number and shaping panicle architecture. A novel favourable allele, RGN1C, derived from the Or‐I group in wild rice affected panicle architecture by means longer panicles. Identification of RGN1 provides a theoretical basis for understanding the molecular mechanism of lateral grain formation in rice; RGN1 will be an important gene resource for molecular breeding for higher yield. [ABSTRACT FROM AUTHOR]

Genetic basis and network studies underlying synergistic biomass accumulation of roots and shoots (SBA) are conducive for rational design of high-biomass rice breeding. In this study, association signals for root weight, shoot weight, and the ratio of root-to-shoot mass (R/S) were identified using 666 rice accessions by genome-wide association study, together with their sub-traits, root length, root thickness and shoot length. Most association signals for root weight and shoot weight did not show association with their sub-traits. Based on the results, we proposed a top-to-bottom model for SBA, i.e. root weight, shoot weight and R/S were determined by their highest priority in contributing to biomass in the regulatory pathway, followed by a lower priority pathway for their sub-traits. Owing to 37 enriched clusters with more than two association signals identified, the relationship among the six traits could be also involved in linkage and pleiotropy. Furthermore, a discrimination of pleiotropy and LD at sequencing level using the known gene OsPTR9 for root weight, R/S and root length was provided. The results of given moderate correlation between traits and their corresponding sub-traits, and moderate additive effects between a trait and the accumulation of excellent alleles corresponding to its sub-traits supported a bottom-to-top regulation model for SBA. This model depicted each lowest-order trait (root length, root thickness and shoot length) was determined by its own regulation loci, and competition among different traits, as well as the pleiotropy and LD. All above ensure the coordinated development of each trait and the accumulation of the total biomass, although the predominant genetic basis of SBA is still indistinguishable. The presentation of the above two models and evidence of this study shed light on dissecting the genetic architecture of SBA. [ABSTRACT FROM AUTHOR]

Summary: Panicle number (PN) is one of the three yield components in rice. As one of the most unstable traits, the dynamic change in tiller number (DCTN) may determine the final PN. However, the genetic basis of DCTN and its relationship with PN remain unclear. Here, 377 deeply re‐sequenced rice accessions were used to perform genome‐wide association studies (GWAS) for tiller/PN. It was found that the DCTN pattern rather than maximum tiller number or effective tiller ratio is the determinant factor of high PN. The DCTN pattern that affords more panicles exhibits a period of stable tillering peak between 30 and 45 days after transplant (called DT30 and DT45, respectively), which was believed as an ideal pattern contributing to the steady transition from tiller development to panicle development (ST‐TtP). Consistently, quantitative trait loci (QTL) expressed near DT30−DT45 were especially critical to the rice DCTN and in supporting the ST‐TtP. The spatio‐temporal expression analysis showed that the expression pattern of keeping relatively high expression in root at 24:00 (R24‐P2) from about DT30 to DT45 is a typical expression pattern of cloned tiller genes, and the candidate genes with R24‐P2 can facilitate the prediction of PN. Moreover, gene OsSAUR27 was identified by an integrated approach combining GWAS, bi‐parental QTL mapping and transcription. These findings related to the genetic basis underlying the DCTN will provide the genetic theory in making appropriate decisions on field management, and in developing new varieties with high PN and ideal dynamic plant architecture. Significance Statement: We reported the patterns and genetic basis of dynamic change in tiller and panicle development in rice using a diverse germplasm population and the GWAS analysis. The results provided the genetic evidence that the tiller development pattern with ideal dynamic plant architecture plays an important role in determining the rice PN, and suggested the novel genetic view in considering the appropriate field management and developing the new rice varieties with ideal dynamic plant architecture. [ABSTRACT FROM AUTHOR]

A robust (long and thick) root system is characteristic of upland japonica rice adapted to drought conditions. Using deep sequencing and large scale phenotyping data of 795 rice accessions and an integrated strategy combining results from high resolution mapping by GWAS and linkage mapping, comprehensive analyses of genomic, transcriptomic and haplotype data, we identified large numbers of QTLs affecting rice root length and thickness (RL and RT) and shortlisted relatively few candidate genes for many of the identified small-effect QTLs. Forty four and 97 QTL candidate genes for RL and RT were identified, and five of the RL QTL candidates were validated by T-DNA insertional mutation; all have diverse functions and are involved in root development. This work demonstrated a powerful strategy for highly efficient cloning of moderate- and small-effect QTLs that is difficult using the classical map-based cloning approach. Population analyses of the 795 accessions, 202 additional upland landraces, and 446 wild rice accessions based on random SNPs and SNPs within robust loci suggested that there could be much less diversity in robust-root candidate genes among upland japonica accessions than in other ecotypes. Further analysis of nucleotide diversity and allele frequency in the robust loci among different ecotypes and wild rice accessions showed that almost all alleles could be detected in wild rice, and pyramiding of robust-root alleles could be an important genetic characteristic of upland japonica. Given that geographical distribution of upland landraces, we suggest that during domestication of upland japonica, the strongest pyramiding of robust-root alleles makes it a unique ecotype adapted to aerobic conditions. [ABSTRACT FROM AUTHOR]

The production and use of many heavy meal contained materials almost inevitably release cadmium (Cd) into environment, generating Cd pollutants with adverse impacts on food and human health. Developing an effective method for Cd concentration evaluation in food crops could be an effective approach for toxicity prediction and pollution control. Here, we exploited the genotype-to-phenotype relationship of maize kernel Cd accumulation at whole-genome level, and developed genome-wide association study (GWAS) assisted genomic-enabled prediction (GP) models using machine learning and linear statistical methods. In benchmark tests, marker density and training populations were key parameters in determining GP baseline precision. With optimized parameters, three statistical methods, including Bayes A, ridge regression–best linear unbiased prediction (rrBLUP) and random forest (RF), showed the highest prediction accuracy (Bayes A, 0.83; rrBLUP, 0.89; RF, 0.75) with 100 iterations of cross-validation. In field trial, GP models with rrBLUP performed better than Bayes A and RF, with a higher GP accuracy (r MG) and lower mean absolute error value. Integrating GP with GWAS can be implemented as an effective strategy for accurate evaluation of Cd concentration, which could provide useful guidelines for accelerating the selection and breeding cycle of low-Cd food crops and addressing the environmental Cd contamination problem. [Display omitted] • An innovative approach was developed for food crop Cd contamination management. • GWAS-assisted genomic prediction provides an effective strategy to predict ZmKCd. • GP model demonstrated superior prediction accuracy (r MG = 0.89) for ZmKCd prediction. [ABSTRACT FROM AUTHOR]

Background: The speciation and fast global domestication of bread wheat have made a great impact on three subgenomes of bread wheat. DNA base composition is an essential genome feature, which follows the individual-strand base equality rule and [AT]-increase pattern at the genome, chromosome, and polymorphic site levels among thousands of species. Systematic analyses on base compositions of bread wheat and its wild progenitors could facilitate further understanding of the evolutionary pattern of genome/subgenome-wide base composition of allopolyploid species and its potential causes. Results: Genome/subgenome-wide base-composition patterns were investigated by using the data of polymorphic site in 93 accessions from worldwide populations of bread wheat, its diploid and tetraploid progenitors, and their corresponding reference genome sequences. Individual-strand base equality rule and [AT]-increase pattern remain in recently formed hexaploid species bread wheat at the genome, subgenome, chromosome, and polymorphic site levels. However, D subgenome showed the fastest [AT]-increase across polymorphic site from Aegilops tauschii to bread wheat than that on A and B subgenomes from wild emmer to bread wheat. The fastest [AT]-increase could be detected almost all chromosome windows on D subgenome, suggesting different mechanisms between D and other two subgenomes. Interestingly, the [AT]-increase is mainly contributed by intergenic regions at non-selective sweeps, especially the fastest [AT]-increase of D subgenome. Further transition frequency and sequence context analysis indicated that three subgenomes shared same mutation type, but D subgenome owns the highest mutation rate on high-frequency mutation type. The highest mutation rate on D subgenome was further confirmed by using a bread-wheat-private SNP set. The exploration of loci/genes related to the [AT] value of D subgenome suggests the fastest [AT]-increase of D subgenome could be involved in DNA repair systems distributed on three subgenomes of bread wheat. Conclusions: The highest mutation rate is detected on D subgenome of bread wheat during domestication after allopolyploidization, leading to the fastest [AT]-increase pattern of D subgenome. The phenomenon may come from the joint action of multiple repair systems inherited from its wild progenitors. [ABSTRACT FROM AUTHOR]