Progeny Populations Research Articles

Association of T2/S-RNase With Self-Incompatibility of Japanese Citrus Accessions Examined by Transcriptomic, Phylogenetic, and Genetic Approaches.

Several citrus varieties show gametophytic self-incompatibility (GSI), which can contribute to seedless fruit production in several cultivars. This study investigated the genes regulating this trait through RNA-seq performed using styles collected from the flowers of Japanese citrus cultivars ‘Hyuganatsu,' ‘Tosabuntan,' ‘Hassaku,' ‘Banpeiyu,' and ‘Sweet Spring'. We screened the transcripts of putative T2 RNases, i.e., the protein family including all S-RNases from S-RNase-based GSI plants, and constructed a phylogenetic tree using the screened T2 RNases and S-RNases retrieved from citrus genome databases and a public database. Three major clusters (class I–III) were formed, among which, the class III cluster contained family specific subclusters formed by S-RNase and a citrus-specific cluster monophyletic to the S-RNase clusters. From the citrus class III cluster, six transcripts were consistent with the S haplotypes previously determined in Japanese citrus accessions, sharing characteristics such as isoelectric point, extracellular localization, molecular weight, intron number and position, and tissue-specific expression with S-RNases. One T2 RNase gene in self-incompatible Hyuganatsu was significantly down-regulated in the styles of a self-compatible mutant of Hyuganatsu in RNA-seq and qPCR analyses. In addition, the inheritance pattern of some T2 RNase genes was consistent with the pattern of the S haplotype in the progeny population of Hyuganatsu and Tosabuntan. As all results supported citrus self-incompatibility being based on S-RNase, we believe that six T2 RNase genes were S-RNases. The homology comparison between the six T2 RNases and S-RNases recently reported in Chinese citrus revealed that three out of six T2 RNases were identical to S-RNases from Chinese citrus. Thus, the other three T2 RNases were finally concluded to be novel citrus S-RNases involved in self-incompatibility.

Film seeds coating with hexane extracts from Illicium verum Hook.f. and Syzygium aromaticum (L.) Merrill & Perry for controlling Callosobruchus maculatus (F.) and Callosobruchus chinensis L.

The application of film seed coating with some plant extracts against stored insect pests was an alternative approach for insect protection instead of using chemical insecticides. The overuse of insecticides has contributed to both human health and environmental problems. The hexane extracts of Illicium verum (HS) and Syzygium aromaticum (HC) were evaluated against bruchid beetles (Callosobruchus maculatus and Callosobruchus chinensis). The insecticidal activities and enhancing seed germination after being coated by various concentrations of extracts, purified fraction (PF) of extracts, standard chemicals of PF, fipronil insecticide (FI), and coating agent groups were evaluated after stored. Both HS and HC at 3% concentrations were more effective against C. maculatus than C. chinensis with LT50 values of 1.60-1.90 and 3.44-3.62 h, respectively. They could also kill those insects with a higher number than that of standards. The HS and HC could inhibit the progeny population of those insects over 95.6% with no significant difference compared to the FI group. The eugenol standard was the most effective and completely inhibited the emergence compared with trans-anethol standard and PFs. The seed that was coated with 1% of HS and stored at 4 °C for 6 months showed no effect on seed germination with no significant difference between FI and control groups. The application of 1% of HS incorporated in the film seed coating against bruchid beetles and did not affect seed germination quality after 6 months. © 2021 Society of Chemical Industry.

Restoring Fertility for Novel Interspecific Hybrids between Kalanchoe garambiensis and K. nyikae Using Colchicine Treatment.

Interspecific hybridization is an effective strategy in Kalanchoe breeding programs for the introduction of new traits. Wild species within the Kalanchoe genus are valuable genetic resources for providing new horticulture traits and to improve environmental adaptations. However, reproductive barriers associated with fertilization and hybrid sterility must be overcome to produce fertile hybrid progenies. To approach the breeding objectives for Kalanchoe cut flower cultivars with long stem traits and adaptation to tropical/subtropical regions, a tropical species endemic to Taiwan, Kalanchoe garambiensis Kudo, was used as a parent to cross with other long stem Kalanchoe species. Reciprocal crossing was effective in overcoming interspecific unilateral incompatibility in our crossed pairs. One superior hybrid, ‘103-1’, produced capsules without seeds by selfing and backcrossing with pollens from either parent. Other than the seedless trait, failure of pollen releasing from anther, pollen aggregation and no pollen germination in ‘103-1’ suggested its F1 sterility. Colchicine treatments on apical buds of ‘103-1’ successfully overcame potential meiotic abnormalities by doubling ploidy. For the first time, fertile interspecific hybrids of K. garambiensis and K. nyikae Engler were generated. The fertile hybrid has further produced progeny populations by crossing with K. nyikae or K. blossfeldiana von Poelln, ‘Ida’.

Biased Pol II fidelity contributes to conservation of functional domains in the Potato spindle tuber viroid genome.

Accurate calculation of mutation rates for viruses and viroids is necessary for evolutionary studies and to evaluate adaptation potential. However, estimation of in vivo mutation rates is complicated by selection, which leads to loss or proliferation of certain mutations. To minimize this concern, lethal mutations, including nonsense and non-synonymous mutations, have been used to determine mutation rates for several viruses and viroids, including Potato spindle tuber viroid (PSTVd). However, this approach has limitations, including focus on a relatively small number of genome sites and the possibility that mutations may not actually be lethal or may be maintained by wild type individuals. To avoid selection bias altogether, we sequenced minus-strand PSTVd dimers from concatemeric replication intermediates. The underlying rationale is that mutations found in only one of the monomers were likely generated de novo during RNA polymerase II (Pol II) transcription of the circular plus-strand RNA genome. This approach yielded an apparent Pol II error rate of ~1/1837 nucleotides per transcription cycle, and an estimated mutation rate of ~1/919 nucleotides for a single replication cycle. Remarkably, de novo mutations were nearly absent from the most conserved, replication-critical regions of the PSTVd genome, suggesting that sequence conservation is a consequence of both essential function and template optimization for greater Pol II fidelity. Such biased fidelity may constitute a novel strategy to ensure population success while allowing abundant sampling of sequence space in other genome regions. Comparison with variants in progeny populations derived from a cloned, wild type PSTVd master sequence revealed that most de novo mutations were lost through selection.

Identification of superior parental lines for biparental crossing via genomic prediction.

A parental selection approach based on genomic prediction has been developed to help plant breeders identify a set of superior parental lines from a candidate population before conducting field trials. A classical parental selection approach based on genomic prediction usually involves truncation selection, i.e., selecting the top fraction of accessions on the basis of their genomic estimated breeding values (GEBVs). However, truncation selection inevitably results in the loss of genomic diversity during the breeding process. To preserve genomic diversity, the selection of closely related accessions should be avoided during parental selection. We thus propose a new index to quantify the genomic diversity for a set of candidate accessions, and analyze two real rice (Oryza sativa L.) genome datasets to compare several selection strategies. Our results showed that the pure truncation selection strategy produced the best starting breeding value but the least genomic diversity in the base population, leading to less genetic gain. On the other hand, strategies that considered only genomic diversity resulted in greater genomic diversity but less favorable starting breeding values, leading to more genetic gain but unsatisfactorily performing recombination inbred lines (RILs) in progeny populations. Among all strategies investigated in this study, compromised strategies, which considered both GEBVs and genomic diversity, produced the best or second-best performing RILs mainly because these strategies balance the starting breeding value with the maintenance of genomic diversity.

Trends in family and individual genotype variance components and broad-sense heritability among unselected South African sugarcane breeding populations

Family evaluation has been adopted to improve selection in the early stages of sugarcane breeding. However, little knowledge is available for comparing families to genotypes among diverse sugarcane populations. The objectives were to determine and compare trends between family and individual genotype (genotype) variance components and broad-sense heritability (H) among unselected sugarcane progeny populations and evaluate the implications for sugarcane breeding. Data for stalk numbers, stalk height and stalk diameter used to calculate cane yield were measured from trials established in the Midlands, coastal and irrigated sites between 2010 and 2015. Family and individual genotype variance were significant (p < 0.001) for assessed traits indicating high family and genotype variability. Family variance was higher than genotype variance suggesting that family evaluation provided more insight into population genetic variability. Families had higher H estimates (21 to 96%) than genotypes (0 to 31%), indicating that selecting superior families would be more efficient than selecting genotypes. Family evaluation followed by efficient genotype selection within superior families is expected to increase genetic gains for cane yield. Populations with high family variance and H showed higher genetic variability and discriminating ability for cane yield among families.

Construction of a breeding parent population of Populus tomentosa based on SSR genetic distance analysis

Parent selection is the core of hybrid breeding. The breeding strategy involving the parental identification of superior open-pollinated progeny of Populous tomentosa germplasm resources can significantly improve the efficiency of parental matching. However, due to some factors such as loose powdering time and pollen competitiveness, the offspring derived from open-pollination families which do not undergo completely random mating. Although hybrid combinations based on the male identification method have a high combining ability, this method cannot easily cover the mating combinations of all male and female specimens in the germplasm bank. In addition, the performance of superior plants in open-pollinated families also affects the selection result. If the trait performance value is higher than the population average, then the special combining ability of the reconstructed hybrid combination may be overestimated. Obtaining a solution to the above problems is of great significance for improving the efficiency and accuracy of selecting hybrid parents of P. tomentosa. In this study, 24 pairs of SSR (Simple Sequence Repeats) molecular markers were used to analyze the genetic differentiation of P. tomentosa germplasm resources. The results showed that the genetic variation of the P. tomentosa population was derived from individuals within the provenance, indicating that high genetic diversity is preserved in provenances. The correlation analysis showed that there was a significant positive correlation between the special combining ability of planting height and diameter at breast height (dbh) of the 34 full-sib progeny population and the genetic distance between the parents. Then, the genetic distance between 18 female plants with high fertility and 68 male plants with large pollen quantity was analyzed using this correlation. Fifteen female parents and 12 male parents were screened out, and 52 hybrid combinations with high specific combining ability for growth traits were predicted. Furthermore, for the male parent identification of superior individual plants, we constructed the breeding parent population including 10 female parents and 5 male parents, generating 14 hybrid combinations with potentially high combining ability. The results of the hybridization test showed that the specific combining ability of plant height and dbh was significantly higher than the controlled pollination. Moreover, genetic distance and paternal identification can be used to rapidly and efficiently construct hybrid parent combinations and breeding parent populations.

Inheritance Pattern of Fruit Color and Shape in Multi-Pistil and Purple Tomato Crossing

Purple tomato is the only cultivated tomato containing anthocyanin inside the fruit, while multi-pistil tomato has a unique shape and the ability to be split into smaller parts without damaging the whole fruit. Purple tomato breeding is a new direction of agriculture research to enrich antioxidant fruit, which nowadays is increasingly in demand. The objective of this research was to obtain multi-pistil tomato fruit containing anthocyanin (purple colored), also to discover the inheritance patterns and heritability of qualitative traits related to fruit color and shape obtained from multi-pistil and purple tomato crossing. This research was conducted using seven populations consisted of 2 parental populations (Multi-pistil Tomato and Purple Tomato), 2 first progeny populations (F1 and F1 Reciprocal), 2 backcross populations (BC1.1 and BC1.2), and second progeny population (F2). The result showed that pistil type, unripe fruit color, ripe fruit color, fruit shape and fruit type were inherited autosomally. The inheritance pattern of the traits followed the epistasis gene interaction with moderate to high heritability value.

Advances in the methods of detecting interspecific gene introgression and their applications

<p indent="0mm">With the proceeding of lineage sorting, gene flow gradually decays among progeny populations that are derived from splitting of a common ancestral population, and may probably continue till the phase of speciation. The differences between interspecific genome sequences or between interspecific population gene frequencies partially record these dynamics of historical and contemporary demography and occurrences, and hence inferences on these events can be attained from analyses of interspecific genomic sequences or gene frequencies. Here, we systematically discussed the methods of detecting interspecific gene introgression, including the approaches based on the differences among interspecific gene frequencies (<italic>F</italic>_{<italic>st</italic>}, LD, STRUCTURE, AFS, TreeMix) and the differences of interspecific DNA sequences (ABBA-BABA, IM, IIM, ABC). We discussed the principles and limits of these methods. Relaxations of some important assumptions underlying these methods remain open questions in the future, including the effects of recombination, the separate contribution of gamete vs. zygote dispersal to gene introgression, the interaction of mating system with gene flow, and the impediment to speciation arising from introgression of adaptive genes. Clarifications of these effects would aid in our deep understanding of the process of speciation.

Recurrent Selection with Glufosinate at Low Rates Reduces the Susceptibility of a Lolium perenne ssp. multiflorum Population to Glufosinate

Repeated applications of herbicides at the labelled rates have often resulted in the selection and evolution of herbicide-resistant weeds capable of surviving the labelled and higher rates in subsequent generations. However, the evolutionary outcomes of recurrent herbicide selection at low rates are far less understood. In this study of a herbicide-susceptible population of Lolium perenne ssp. multiflorum, we assessed the potential for low glufosinate rates to select for reduced susceptibility to the herbicide, and cross-resistance to herbicides with other modes of action. Reduced susceptibility to glufosinate was detected in progeny in comparison with the parental population following three rounds of selection at low glufosinate rates. Differences were mainly observed at the 0.5X, 0.75X, and 1X rates. Comparing the parental susceptible population and progeny from the second and third selection cycle, the percentage of surviving plants increased to values of LD50 (1.31 and 1.16, respectively) and LD90 (1.36 and 1.26, respectively). When treated with three alternative herbicides (glyphosate, paraquat, and sethoxydim), no plants of either the parental or successive progeny populations survived treatment with 0.75X or higher rates of these herbicides. The results of this study provide clear evidence that reduced susceptibility to glufosinate can evolve in weed populations following repeated applications of glufosinate at low herbicide rates. However, the magnitude of increases in resistance levels over three generations of recurrent low-rate glufosinate selection observed is relatively low compared with higher levels of resistance observed in response to low-rate selection with other herbicides (three fold and more).

Comparing Genotypic and Phenotypic Variation of Selfed and Outcrossed Progeny of Hemp

Feminized hemp seed producers often use selfing to maintain a strain name; however, selfing may lead to inferior plants for cannabidiol (CBD) production. Using three different hemp strains as parents [Candida (CD-1), Dinamed CBD, and Abacus], two outcrosses [Candida (CD-1) × Abacus and Dinamed CBD × Candida (CD-1)] and one self-cross [Candida (CD-1) × Candida (CD-1)] were conducted to produce feminized seed. Progeny from the self-cross were significantly smaller and had less yield than outcrossed progeny. Selfed progeny were variegated and highly variable for total dry weight and floral dry weight. Discriminant analysis of principal components (DAPC) using amplified fragment length polymorphism (AFLP) separated the three progeny populations and showed that outcrossed populations clustered closer to the maternal parent, possibly the result of a maternal effect. Analysis of molecular variance (AMOVA) indicated that most variation (74.5%) was within populations, because the progeny from all three populations are half-siblings of each other. The selfed progeny population had lower expected heterozygosity (He = 0.085) than each of the outcrossed progeny populations (He ≈ 0.10). These results suggest that selfed progeny may demonstrate inbreeding depression resulting from enhanced expression of homozygous recessive traits. It may be beneficial for feminized seed producers to use outcrossing instead of selfing to generate feminized seed for CBD production.

Fine mapping of the BnUC2 locus related to leaf up-curling and plant semi-dwarfing in Brassica napus

BackgroundStudies of leaf shape development and plant stature have made important contributions to the fields of plant breeding and developmental biology. The optimization of leaf morphology and plant height to improve lodging resistance and photosynthetic efficiency, increase planting density and yield, and facilitate mechanized harvesting is a desirable goal in Brassica napus.ResultsHere, we investigated a B. napus germplasm resource exhibiting up-curled leaves and a semi-dwarf stature. In progeny populations derived from NJAU5737 and Zhongshuang 11 (ZS11), we found that the up-curled leaf trait was controlled by a dominant locus, BnUC2. We then fine mapped the BnUC2 locus onto an 83.19-kb interval on chromosome A05 using single nucleotide polymorphism (SNP) and simple sequence repeat (SSR) markers. We further determined that BnUC2 was a major plant height QTL that explained approximately 70% of the phenotypic variation in two BC5F3 family populations derived from NJAU5737 and ZS11. This result implies that BnUC2 was also responsible for the observed semi-dwarf stature. The fine mapping interval of BnUC2 contained five genes, two of which, BnaA05g16700D (BnaA05.IAA2) and BnaA05g16720D, were revealed by comparative sequencing to be mutated in NJAU5737. This result suggests that the candidate gene mutation (BnaA05g16700D, encoding Aux/IAA2 proteins) in the conserved Degron motif GWPPV (P63S) was responsible for the BnUC2 locus. In addition, investigation of agronomic traits in a segregated population indicated that plant height, main inflorescence length, and branching height were significantly reduced by BnUC2, whereas yield was not significantly altered. The determination of the photosynthetic efficiency showed that the BnUC2 locus was beneficial to improve the photosynthetic efficiency. Our findings may provide an effective foundation for plant type breeding in B. napus.ConclusionsUsing SNP and SSR markers, a dominant locus (BnUC2) related to up-curled leaves and semi-dwarf stature in B. napus has been fine mapped onto an 83.19-kb interval of chromosome A05 containing five genes. The BnaA05.IAA2 is inferred to be the candidate gene responsible for the BnUC2 locus.

Localization of quantitative trait loci for cucumber fruit shape by a population of chromosome segment substitution lines

Cucumber fruit shape, a significant agronomic trait, is controlled by quantitative trait loci (QTLs). Feasibility of chromosome segment substitution lines (CSSLs) is well demonstrated to map QTLs, especially the minor-effect ones. To detect and identify QTLs with CSSLs can provide new insights into the underlying mechanisms regarding cucumber fruit shape. In the present study, 71 CSSLs were built from a population of backcross progeny (BC4F2) by using RNS7 (a round-fruit cucumber) as the recurrent parent and CNS21 (a long-stick-fruit cucumber) as the donor parent in order to globally detect QTLs for cucumber fruit shape. With the aid of 114 InDel markers covering the whole cucumber genome, 21 QTLs were detected for fruit shape-related traits including ovary length, ovary diameter, ovary shape index, immature fruit length, immature fruit diameter, immature fruit shape index, mature fruit length, mature fruit diameter and mature fruit shape index, and 4 QTLs for other traits including fruit ground and flesh color, and seed size were detected as well. Together our results provide important resources for the subsequent theoretical and applied researches on cucumber fruit shape and other traits.

UJI POLIMORPIK DAN HETEROZIGOSITAS PADA PROGENI F4 KEDELAI (Glycine max (L.) Merril) TAHAN SALIN DENGAN MENGGUNAKAN MARKA SSR (Simple Sequence Repeats)

SSR marker has some merits such as quickness, simplicity, rich polymorphism and stability, thus being widely applied in genetic diversity analysis, molecular map construction and gene mapping. the purpose of this study was to determine polymorpic test and heterozygosity in F4 soybean (Glycine max (L.) Merril) progeni saline resistant characters using SSR (Simple Sequence Repeats) markers. This research was conducted in Biomolecular Laboratory, Socfindo Seed Production Laboratory (SSPL), Kebun Bangun Bandar Village Martebing District Dolok Masihul Regency Serdang Bedagai on December-May 2017. The number of samples were used 44. The five SSR primers (QS080465, QS1101, QS1112, QS100011, and Sat_091) used were specific primers, with a band pattern that was clearly visible around one or two bands. The percentage of polymorphic primers (PLP) of these three populations is high, all populations with a PLP of 100% of the saline resistant character. The effective allele number (Ne) of 7,160 for the progeny population is lower than the number of observed alleles (Na) of 10,000 which means that many progeny individuals are homozygous. The expected heterozygosity (He) value of 0.854 in the progeny population was higher than the observed heterozygosity (Ho) value of 0.027. The overall average observed heterozygosity (Ho) was 0.009 lower than the overall expected heterozygosity (He) of 0.61. This means that each character has a low heterozygosity.Keywords: Progeny F4, soybean, SSR, saline resistant, polymorphic, heterozygosity

Responses of Total Biomass, Shoot Dry Weight, Yield and Yield Components of Jerusalem Artichoke (Helianthus tuberosus L.) Varieties under Different Terminal Drought Duration

As a secondary crop planting in the double-cropping system, terminal drought is the major constraint of Jerusalem artichoke production in the rainfed area. This study aims to estimate the effects of different durations of terminal drought on total biomass, tuber yields, harvest index, yield components, and to identify high yield potential and low yield reduction genotypes for the varietal improvement program. A split-plot design with four replications was conducted under field experiment for two years. Three drought durations including non-drought stress (SD0), drought from 60 and 45 days after transplanting until harvest (SD1 and SD2, respectively), were assigned in main plots and six genotypes were arranged in subplots. Crop parameters were greater decreased under a long-drought duration than under short-drought duration. The genotypes were identified; HEL256, JA37 and JA125 had high yield potential under SD0 conditions, whereas there was high yield reduction under drought conditions. In contrast, JA60 and HEL253 were identified as low yield potential and low yield reduction genotypes. This information suggested that high yield potential genotypes and low yield reduction genotypes should be selected and generated progeny population for improvement of new varieties with high yield potential and low yield reduction for growing in terminal drought-prone environments.

Population genetic diversity of mud crab (Scylla paramamosain) from southeast coastal regions of China based on mitochondrial COI gene sequence.

Mud crab (Scylla paramamosain) is a native and economically important species in East Asia. In order to provide a comprehensive genetic background for the resource protection and management in this species, the genetic diversity and population structure of S. paramamosain were analyzed based on mitochondrial cytochrome oxidase subunit I (COI) gene sequence. Totally, 599 individuals were sampled from 20 populations, including 18 wild and two cultured populations from five provinces along southeastern coast of China. After the sequencing of a 638bp fragment of COI gene, 84 variable sites were found and no insertion or deletion was detected. The H2 (haplotype 2) was the dominant hapolotye shared by 301 individuals (50.3% of all individuals) and existed in all localities. In addition, a high percent of unique haplotypes (53 of 93 haplotyoes) was found. The average nucleotide diversity (π) of all populations was 0.00194, ranging from 0.00010 (NHF1) to 0.00305 (SHCM). The haplotype diversity (h) ranged from 0.067 (NHF1) to 0.876 (CM) with an average 0.738. All of the populations showed high h (>0.5) except NHF1. Genetic distance ranged from 0.00063 to 0.00337 between populations and from 0.00010 to 0.00374 within populations. The molecular variance analysis (AMOVA) showed that the total genetic variation mainly occurred within populations (99.68%) and only 0.32% was contributed by among populations variation. No significant genetic differentiation was observed among all wild populations except that between BA and SHCM (Fst=0.0.05707, P<0.05), indicating a low level of genetic differentiation among localities. It is worth to note that two progeny population (HNF1 and NHF1) showed significantly different genetic variation, which suggested that a large quantity of parents could help to improve the genetic diversity of progeny populations.

A pentaploid-based linkage map of the ancestral octoploid strawberry Fragaria virginiana reveals instances of sporadic hyper-recombination

The first high-resolution genetic linkage map of the ancestral octoploid (2n = 8x = 56) strawberry species, Fragaria virginiana, was constructed using segregation data obtained from a pentaploid progeny population. This novel mapping population of size 178 was generated by crossing highly heterozygous F. virginiana hybrid “LB48” as a paternal parent with diploid (2n = 2x = 14) Fragaria vesca “Hawaii 4”. The LB48 linkage map comprises 6055 markers genotyped on the Axiom® IStraw90 strawberry SNP array. The map consists of 28 linkage groups (LGs) organized into seven homoeology groups of four LGs each, and excludes a small 29th LG of undefined homoeology. One member of each homoeology group was assignable to an “A” subgenome associated with ancestral diploid Fragaria vesca, while no other subgenomes were defined. Despite an intriguing discrepancy within homoeology group VI, synteny comparisons with the previously published Fragaria ×ananassa DA × MO linkage map revealed substantial agreement. Following initial map construction, examination of crossover distributions revealed that six of the total 5162 (=29 chromosomes/individual × 178 individuals) chromosomes making up the data set exhibited abnormally high crossover counts, ranging from 15 to 48 crossovers per chromosome, as compared with the overall mean of 0.66 crossovers per chromosome. Each of these six hyper-recombinant (HypR) chromosomes occurred in a different LG and in a different individual. When calculated upon exclusion of the six HypR chromosomes, the canonical (i.e., broadly representative) LB48 map had 1851 loci distributed over a total map length of 1873 cM, while their inclusion increased the number of loci by 130, and the overall map length by 91 cM. Discovery of these hyper-recombinant chromosomes points to the existence of a sporadically acting mechanism that, if identified and manipulable, could be usefully harnessed for multiple purposes by geneticists and breeders.

Ex situ conservation of Pinus koraiensis can preserve genetic diversity but homogenizes population structure

Pinus koraiensis is a conifer species of ecological and economic importance in northeast China that has been excessively exploited in recent years. A clonal seed orchard (CSO) was established including potentially genetically differentiated provenances from the whole distribution area, we applied nine simple sequence repeat (SSR) makers to study the genetic diversity and population structure of six maternal populations as well as their progeny populations. The results showed a high genetic diversity in both maternal and progeny populations, with the average expected heterozygosity of 0.617 and 0.632, respectively. The level of genetic diversity in the progeny populations was slightly higher than that in the maternal populations, and almost all diversity descriptors were correlated between maternal and progeny populations, indicating that the CSO could preserve the established species’ gene pool. An overall low level of genetic differentiation of P. koraiensis (FST = 0.029 and 0.025 for maternal and progeny populations) was found. The six maternal populations clustered into two groups by Bayesian cluster analysis with the two northernmost populations comprising one group and the other four populations as another genetically differentiated group, potentially indicating regional adaptation. The northern group had significantly higher levels of within population diversity. Population structure was not evident anymore in the progeny populations, suggesting that mating among differentiated provenances within the CSO homogenized the different gene pools, although differences in diversity were still maintained. These results will inform efforts for the conservation and management of P. koraiensis and provide guidance for future studies of population genetics and breeding programs.

Linking crop traits to transcriptome differences in a progeny population of tetraploid potato

BackgroundPotato is the third most consumed crop in the world. Breeding for traits such as yield, product quality and pathogen resistance are main priorities. Identifying molecular signatures of these and other important traits is important in future breeding efforts. In this study, a progeny population from a cross between a breeding line, SW93–1015, and a cultivar, Désirée, was studied by trait analysis and RNA-seq in order to develop understanding of segregating traits at the molecular level and identify transcripts with expressional correlation to these traits. Transcript markers with predictive value for field performance applicable under controlled environments would be of great value for plant breeding.ResultsA total of 34 progeny lines from SW93–1015 and Désirée were phenotyped for 17 different traits in a field in Nordic climate conditions and controlled climate settings. A master transcriptome was constructed with all 34 progeny lines and the parents through a de novo assembly of RNA-seq reads. Gene expression data obtained in a controlled environment from the 34 lines was correlated to traits by different similarity indices, including Pearson and Spearman, as well as DUO, which calculates the co-occurrence between high and low values for gene expression and trait. Our study linked transcripts to traits such as yield, growth rate, high laying tubers, late and tuber blight, tuber greening and early flowering. We found several transcripts associated to late blight resistance and transcripts encoding receptors were associated to Dickeya solani susceptibility. Transcript levels of a UBX-domain protein was negatively associated to yield and a GLABRA2 expression modulator was negatively associated to growth rate.ConclusionIn our study, we identify 100’s of transcripts, putatively linked based on expression with 17 traits of potato, representing both well-known and novel associations. This approach can be used to link the transcriptome to traits. We explore the possibility of associating the level of transcript expression from controlled, optimal environments to traits in a progeny population with different methods introducing the application of DUO for the first time on transcriptome data. We verify the expression pattern for five of the putative transcript markers in another progeny population.

Potential of Genome-Wide Association Studies and Genomic Selection to Improve Productivity and Quality of Commercial Timber Species in Tropical Rainforest, a Case Study of Shorea platyclados

Shorea platyclados (Dark Red Meranti) is a commercially important timber tree species in Southeast Asia. However, its stocks have dramatically declined due, inter alia, to excessive logging, insufficient natural regeneration and a slow recovery rate. Thus, there is a need to promote enrichment planting and develop effective technique to support its rehabilitation and improve timber production through implementation of Genome-Wide Association Studies (GWAS) and Genomic Selection (GS). To assist such efforts, plant materials were collected from a half-sib progeny population in Sari Bumi Kusuma forest concession, Kalimantan, Indonesia. Using 5900 markers in sequences obtained from 356 individuals, we detected high linkage disequilibrium (LD) extending up to &gt;145 kb, suggesting that associations between phenotypic traits and markers in LD can be more easily and feasibly detected with GWAS than with analysis of quantitative trait loci (QTLs). However, the detection power of GWAS seems low, since few single nucleotide polymorphisms linked to any focal traits were detected with a stringent false discovery rate, indicating that the species’ phenotypic traits are mostly under polygenic quantitative control. Furthermore, Machine Learning provided higher prediction accuracies than Bayesian methods. We also found that stem diameter, branch diameter ratio and wood density were more predictable than height, clear bole, branch angle and wood stiffness traits. Our study suggests that GS has potential for improving the productivity and quality of S. platyclados, and our genomic heritability estimates may improve the selection of traits to target in future breeding of this species.