Bailian Li

Population genomic analysis of gibberellin-responsive long non-coding RNAs in Populus

Long non-coding RNAs (lncRNAs) participate in a wide range of biological processes, but lncRNAs in plants remain largely unknown; in particular, we lack a systematic identification of plant lncRNAs involved in hormone responses. Moreover, allelic variation in lncRNAs remains poorly characterized at a large scale. Here, we conducted high-throughput RNA-sequencing of leaves from control and gibberellin (GA)-treated Populus tomentosa and identified 7655 reliably expressed lncRNAs. Among the 7655 lncRNAs, the levels of 410 lncRNAs changed in response to GA. Seven GA-responsive lncRNAs were predicted to be putative targets of 18 miRNAs, and one GA-responsive lncRNA (TCONS_00264314) was predicted to be a target mimic of ptc-miR6459b. Computational analysis predicted 939 potential cis-regulated target genes and 965 potential trans-regulated target genes for GA-responsive lncRNAs. Functional annotation of these potential target genes showed that they participate in many different biological processes, including auxin signal transduction and synthesis of cellulose and pectin, indicating that GA-responsive lncRNAs may influence growth and wood properties. Finally, single nucleotide polymorphism (SNP)-based association analysis showed that 112 SNPs from 52 GA-responsive lncRNAs and 1014 SNPs from 296 potential target genes were significantly associated with growth and wood properties. Epistasis analysis also provided evidence for interactions between lncRNAs and their potential target genes. Our study provides a comprehensive view of P. tomentosa lncRNAs and offers insights into the potential functions and regulatory interactions of GA-responsive lncRNAs, thus forming the foundation for future functional analysis of GA-responsive lncRNAs in P. tomentosa.

Genetic Gains of Full-Sib Families from Disconnected Diallels in Loblolly Pine

Abstract Breeding values for the 2nd-cycle of the loblolly pine (Pinus taeda L.) breeding program were analyzed with the NCSUIndustry Tree Improvement Cooperative database to estimate genetic gains and compare different strategies for full-sib deployment. In the disconnected half-diallel mating design used for loblolly pine, six parents within each diallel were crossed to generate 15 full-sib families for general combining ability (GCA) and specific combining ability (SCA) estimates. Parents among disconnected diallels were never crossed, and the SCA and full-sib family breeding values cannot be estimated directly. Using the GCA and SCA estimates from 60 diallels in the Atlantic Coastal region of loblolly pine, genetic gains were estimated in this study for full-sib families within the disconnected diallels and then compared with the potential gains that would be expected if we select parents for full-sib families based on GCA values for all parents within a geographic region. As the dominance variance was found to be much less than the additive variance, the SCA contribution to the full-sib genetic gain was relatively small. Higher full-sib genetic gains were obtained by crossing the best GCA parents from different diallels within a geographic region than selecting only those within diallels. The difference increased with increasing number of selected full-sibs. Results from different selection scenarios, with various selection intensities and relatedness managements, suggest that selection based on GCA from all parents within a geographic region would result in a higher genetic gain for full-sib families in loblolly pine. The deployment of full-sib families are very important for achieving higher genetic gains in a loblolly pine breeding program. But they were not due to the SCA contribution, but rather due to high GCA of best parents in creating these full-sib crosses. The strategies for family and clonal deployment are very attractive based on the data from this study.

Using SSR markers to study the mechanism of 2n pollen formation in Populus × euramericana (Dode) Guinier and P. × popularis

Abstract• Using cytological methods and SSR DNA marker analysis, this study revealed the formation mechanisms and the genetic constitutions of the 2n pollen in Populus × euramericana (Dode) Guinier and P. × popularis.• In P. × euramericana (Dode) Guinier, four abnormalities in microsporogenesis were observed: parallel spindle, fused spindle, tripolar spindle and premature cytokinesis. The first three can lead to first-division restitution (FDR) 2n pollen formation and the last one can form second-division restitution (SDR) 2n pollen. The SSR marker analysis results of parents and their tetraploidy filial generation confirmed that the genetic constitution of 2n pollen produced by P. × euramericana (Dode) Guinier was FDR.• In P. × popularis, three of these abnormalities were observed: parallel spindle, fused spindle and premature cytokinesis. The SSR marker analysis results showed the genetic constitution of 2n pollen produced by P. × popularis was SDR. Natural 2n female gametes in P. × euramericana (Dode) Guinier are reported for the first time. SSR analysis indicated that natural 2n female gametes of P. × euramericana (Dode) Guinier did exist and were fertile, which could be FDR genetic constitution.• The results from this study showed a great potential for using 2n gametes to produce polyploid poplar clones, which can be used effectively for polyploid breeding for poplar species in the section Aigeiros.Résumé• En utilisant des méthodes cytologiques et des analyses avec des marqueurs SSR, cette étude a révélé les mécanismes de formation et la constitution génétique du pollen 2n chez Populus × euramericana (Dode) Guinier et P. × popularis.• Chez P. × euramericana (Dode) Guinier, quatre anomalies dans la microsporogénèse ont été observées : en parallèle broche, broche fusion,tripolaire broche et une cytokinèse prématurée. Les trois premiers peuvent entraîner une première division restitution (FDR) de formation du pollen 2n et le dernier peut former une deuxième division de restitution (SDR) du pollen 2n. Les résultats de l’analyse des marqueurs SSR des parents et de leur descendanta tetraploides ont confirmé que la constitution génétique du pollen 2n produit par P. × euramericana (Dode) Guinier a été FDR.• Dans P. × popularis, trois de ces anomalies ont été observées : en parallèle broche, broche fusion et cytokinèse prématurée. Les résultats de l’analyse de marqueurs SSR ont montré que la constitution génétique du pollen 2n produit par P. × popularis a été SDR. Les gamètes naturelles femelles 2n chez P. × euramericana (Dode) Guinier ont été signalés pour la première fois. Les analyses SSR ont montré que les gamètes naturels femelles 2n de P. × euramericana (Dode) Guinier existaient et étaient fertiles, cela pourrait être la constitution génétique FDR.• Les résultats de cette étude ont montré le grand potentiel de l’utilisation des gamètes 2n pour produire des clones de peuplier polyploïdes, cela peut être utilisé efficacement pour la sélection de polyploïdes pour des espèces de peuplier de la section Aigeiros.

Seed and pollen flow and cline discordance among genes with different modes of inheritance.

The relationships between seed and pollen flow and cline discordance/concordance between cytoplasmic and nuclear genes, with the incorporation of the effects of natural selection, are formulated for one locus with two alleles, under assumptions of random mating, no drift and no mutation. Results show that under certain conditions, the relative roles of seed and pollen flow in shaping cline discordance/concordance are very similar to their roles in influencing population differentiation for selectively neutral markers with different modes of inheritance. Where the disequilibria between cytoplasmic and nuclear genes are of the order similar to selection coefficient, cline discordance/concordance can be predicted from the relative values of the ratio of pollen to seed flow and the ratio of selection coefficients. Where the disequilibria attained by seed and pollen flow are significant, the integrated cytonuclear data are recommended for cline analysis. In both cases, the relative rates of selection coefficients between cytoplasmic and nuclear genes can be roughly estimated according to their characteristic length.

2n egg formation in Populus × euramericana (Dode) Guinier Evidence from nuclear microsatellite analyses

Three synthetic triploid seedlings were derived from a cross between maternal parent Populus × euramericana (Dode) Guinier and Populus nigra var. italica (Moench.) Koehne via embryo rescue by treating female floral buds with colchicine at certain developmental stages before and after pollination, and identified by flow cytometric analyses. A total of 21 microsatellite primers were used to infer the ploidy of gametes forming the hybrids and the underlying meiotic mechanism. The results suggest that 2n eggs originated from the maternal poplar, contributing the extra haploid genome in the triploids. In addition, first division restitution (FDR) 2n eggs were produced in the maternal tree according to the marker genotypes of these triploids. Cytological analyses of megasporogenesis revealed that meiosis of the maternal parent was asynchronous. This cytological evidence suggests that 2n eggs result from FDR after treatment with colchicine, as a portion of megaspore mother cells (MMCs) were within the first division at the post-pollination stage. These results aid in understanding the mechanism of 2n egg formation in poplar and make the utilization of 2n eggs in polyploid poplar breeding more effectively.

On migration load of seeds and pollen grains in a local population

We have extended Wrights model of migration load to hermaphrodite plants showing variation at a single locus with two alleles. The model incorporates independent migration of seeds and pollen grains, the selection at both the haploid gametophyte and the diploid sporophyte stages, and a mixed mating system. The analytical relations between migration load and migration rate of seeds and pollen grains are explicitly formulated. The results show that under certain conditions, seed flow can have a more effect on migration load than pollen flow. Pollen selection at the gametophyte stage cannot substantially affect the migration load at the sporophyte stage. Selection at the diploid sporophyte stage is critical in determining the migration load of pollen grains. The relative migration loads of pollen versus seeds can be approximately estimated in predominantly outcrossing populations by the ratio of pollen flow to twice the seed flow, when the selection coefficient (sT) is greater than, or approximately equal to, the migration rate ([mtilde ]).

Assessment of the ratio of pollen to seed flow in a cline for genetic variation in a quantitative trait

A dispersal–selection cline model is analysed to evaluate the role of the ratio of pollen to seed flow (r) in spatial genetic variation, with a focus on clines in additive and dominant variances of major genes affecting a quantitative trait, assuming one locus with two alleles, no genetic drift and no mutation. It is shown that under weak selection, steady-state departures from the value at Hardy–Weinberg equilibrium (HWE) for genotype frequency (D) and additive variance (ΔVa) generally display a small value on one side of the selection boundary point, a high value around the point, and a moderate value on the other side of the boundary point. A large value of r can enhance formation of this pattern. However, this is not the case for clines in the average effect of a gene substitution (Δα) or in dominance variance (ΔVd), where large values of r can eradicate the clines. Direct use of their values at HWE to approximate the real case is acceptable. There is an expected turning point that divides clines of either additive variance or dominance variance into two subclines, each with a shorter width than that of allele frequency. Integration of these properties can help to indicate the existence of major genes affecting a quantitative trait.

Induction of 2n pollen by colchicine in Populus × popularis and its triploids breeding

Abstract Induction of 2n pollen is a required technique for cultivating polyploid via sexual polyploidy. Orthogonal design or Taguchi Design was applied to select the best treatment process of 2n pollen induction in Populus × popularis from different levels of the meiosis stage of male flower buds, colchicine concentration, times of injection, and interval between injections. Flow cytometry and chromosome counting were used to identify the triploids from the offspring of P. × euramericana. (Dode) Guinier pollinated with induced pollen of P. × popularis. The results showed that high 2n pollen rate can be achieved by selecting the flower buds during diakinesis stage in meiosis, and then injecting 0.6% colchicine 4 times with 2 hours interval. The 2n pollen rate reached 62.10% by this process, and two triploids were obtained, which indicates that it is possible for cultivating triploids via 2n pollen induction by colchicine treatment in poplar. Results and protocol related to 2n pollen induction, polyploid identification and effect of 2n pollen in this study might be applicable in polyploidy breeding in section Aigeiros and Tacamahaca of poplar.

Prediction of wood density breeding values of Pinus taeda elite parents from unbalanced data: A method for adjustment of site and age effects using common checklots

Abstract• Wood density of elite parents of loblolly pine (Pinus taeda L.) was investigated in 6 to 18 year-old progeny trials. The sampling was carried out separately in seven testing regions in the southeastern US. A checklot was the only connection between elite parents planted at different trials in a testing region.• We used a data normalization method suggested for unbalanced designs in cDNA microarray experiments to remove confounding site and age effects using the checklot as a reference sample. Wood density breeding values of parents were predicted by fitting a linear mixed model to the normalized data.• Using the reference samples to remove site and age effects appears to be an effective method for analysis of unbalanced progeny tests data. In general, wood density (kg/m3) decreased from coastal to inland plantings and from the southern to the northern planting. Considerable genetic variation for wood density was detected among these fast-growing elite parents in six of seven testing regions, with half-sib family mean heritabilities ranging from 0.71 to 0.97 within a testing region. With the exception of two regions, checklots were stable across trials in a region, based on regressing the checklot means on trial means.Résumé• La densité du bois de parents d’élite de Pinus taeda L. a été étudiée dans des essais de descendance âgés de 6 à 18 ans. L’échantillonnage a été mené à bonne fin séparément dans sept régions tests du Sud des États-Unis. Le lot a été le seul lien entre parents d’élite plantés dans différents essais dans la région de test.• Nous avons utilisé une méthode de normalisation des données proposée pour des effectifs non équilibrés de puces à CDNA pour éliminer les effets confondus du site et de l’âge, en utilisant le lot comme échantillon de référence. Les valeurs de la densité du bois des parents ont été prédites par ajustement d’un modèle linéaire mixte aux données normalisées.• Utiliser les échantillons références pour enlever les effets de site et de l’âge apparaît être une méthode efficace pour analyser les données non équilibrées d’un test de descendances. En général, la densité du bois (kg/m3) décroît depuis les plantations côtières jusqu’aux plantations des régions intérieures et depuis les plantations du sud jusqu’aux plantations plus au nord. Une variabilité génétique considérable de la densité du bois a été détectée entre ces parents à croissance rapide dans six des sept régions de test, avec des héritabilités moyennes variant de 0,71 à 0,97 dans une région de test. Sur la base d’une régression entre moyennes des lots de référence et moyennes des essais, il a été déterminé qu’à l’exception de deux régions, les lots ont été stables à travers les essais dans une région déterminée.

Dissection of allelic interactions among Pto-miR257 and its targets and their effects on growth and wood properties in Populus

MicroRNAs (miRNAs) have important roles in the regulation of genes; however, for trees few studies have explored the potential impact of the interactions between miRNAs and their target genes. Here, we performed transcript profiling and association genetics (single-SNP, haplotype-based and multi-SNP associations) to study the genetic regulatory relationship of Pto-miR257 and its 12 target genes in 435 individuals of a natural population of Populus tomentosa. Expression profiling of Pto-miR257 and its targets showed a negative relationship between their expression levels. Of the 61 single-nucleotide polymorphisms (SNPs) detected in Pto-miR257, 6 in the pre-mature region strongly affected its secondary stability and 1 in the mature region could alter its target spectrum. Among the 1029 SNPs in the targets, 3 were located in target sites that could change the binding affinity of Pto-miR257. Single-SNP association analysis revealed that SNPs in Pto-miR257 and target genes associated with both growth and wood property traits, in agreement with haplotype-based identifications. Multi-SNP association found that 10 targets shared at least one common trait with Pto-miR257, with phenotypic variance from 0.5 to 8.5%, suggesting a possible internal genetic interaction between them. Epistasis analysis showed significant epistatic interactions among Pto-miR257 and its targets. Therefore, our study demonstrated Pto-miR257 and its 12 targets had roles in wood formation and revealed the genetic interaction network between the miRNA and its targets under additive, dominant and epistatic models. Thus, association genetics can be used to decipher the interactions between miRNAs and their target genes and to help understand the genetic architecture of complex traits.