The wild relative of wheat, Agropyron cristatum (L.) Gaertn. (genome PPPP), acts as an important genetic resource for providing valuable genes for wheat improvement and increasing the diversity of cultivated wheat. In the present study, cytogenetic and molecular tools were used to characterize wheat-A. cristatum 6P derivatives. The novel translocation line Pubing260 exhibiting wider flag leaves and superior spike traits was further characterized and analysed. Cytological studies demonstrated that Pubing260 (2n = 42) contained a T3BL3BS-6PL terminal translocation. We compared molecular markers on chromosomes 6P and 3B and confirmed that the translocated wheat chromosome was 3BS and that the chromosome breakage occurred in bin 3BS9-0.57-0.75. Compared with its recurrent parent Fukuhokomugi, Pubing260 had a wider flag leaf, more spikelets and more grains per spike in two growing seasons. Genetic analysis conducted using BC1F2 and BC2F1 populations suggested that the A. cristatum chromosomal fragment from bin 6PL-0.72-1.00 conferred these potentially valuable agronomic traits. On average, the flag leaf width (FLW), and numbers of grain per spike (GNS), spikelets per spike (SNS) and kernels per spikelet of plants with the translocation were 2 mm wider and 5.1, 0.8 and 0.3 higher, respectively, than those of plants lacking the translocation in segregating populations. Significant and positive correlations were observed among GNS, SNS and FLW. In summary, this study not only reports a novel germplasm that is potentially valuable for wheat improvement but also enriches the genetic resources of wheat.
Rapid growth and high quality have always been important goals pursued for timber forests. Therefore, growth traits and wood properties are the basis of superior materials to select and breed new cultivars. In this study, 42 half-sib families of 31-year-old P. koraiensis trees were used as materials. Nine growth traits (tree height, diameter at breast height, volume, basal diameter, average annual growth of the tree height, under branch height, stem straightness degree, form quotient, and branching angle) and eight wood properties (cellulose contents, hemicellulose contents, holocellulose contents, lignin contents, ash contents, wood density, fiber length and fiber width) were measured and analyzed. The results of an analysis of variance showed that there were extremely significant differences among the families in their growth and wood properties with the exception of the form quotient and wood density; that there were significant differences among block by family for growth traits except for the tree height, basal diameter, under branch height and branching angle; and that there was no significant difference for each growth trait among the blocks. The phenotypic coefficient of variation and heritability of the growth traits ranged from 7.17 to 42.35% and from 0.13 to 0.62, respectively. The phenotypic coefficient of variation and heritability of the wood properties ranged from 10.21 to 50.26% and from 0.67 to 0.92, respectively. There were extremely significantly positive correlations between the tree height, basal diameter, diameter at breast height, volume, under branch height, average annual growth of tree height and form quotient. However, there was no significant correlation between growth traits and wood properties. The result of the principal component analysis indicated that the tree height, diameter at breast height, volume, basal diameter, and cellulose contents, holocellulose contents, and lignin contents could be selected as comprehensive evaluation indices of growth and wood properties, respectively. According to a comprehensive evaluation, when the selection rate was 10%, four families (PK 40, PK 80, PK 42, and PK 71) were selected as elite families based on growth performance; another four families (PK 70, PK 62, PK 52, and PK 44) were selected as elite families based on their wood quality; and finally, four elite families (PK 70, PK 62, PK 61, and PK 40) were selected due to a combination of growth traits and wood properties. This study will provide a theoretical basis for the genetic improvement of fast-growing and high-quality P. koraiensis families.
Flag leaf-related traits (FLRTs) are determinant traits affecting plant architecture and yield potential in wheat (Triticum aestivum L.). In this study, three related recombinant inbred line (RIL) populations with a common female parent were developed to identify quantitative trait loci (QTL) for flag leaf width (FLW), length (FLL), and area (FLA) in four environments. A total of 31 QTL were detected in four environments. Two QTL for FLL on chromosomes 3B and 4A (QFll-3B and QFll-4A) and one for FLW on chromosome 2A (QFlw-2A) were major stable QTL. Ten QTL clusters (C1-C10) simultaneously controlling FLRTs and yield-related traits (YRTs) were identified. To investigate the genetic relationship between FLRTs and YRTs, correlation analysis was conducted. FLRTs were found to be positively correlated with YRTs especially with kernel weight per spike and kernel number per spike in all the three RIL populations and negatively correlated with spike number per plant. Appropriate flag leaf size could benefit the formation of high yield potential. This study laid a genetic foundation for improving yield potential in wheat molecular breeding programs.
Fruit spine size is one of the importantly external quality traits effected the economic value of cucumber fruit. Morphological-cytological observation of the fruit spine size phenotype indicated that large spine formation arises from an increasing of spiny pedestal cell number caused by cell division, and best periods to accurately score fruit spine size trait was 4th day before flowering to 7th day after flowering according the continuous observation. Genetic analysis showed that a single dominant gene determined the fruit spine size trait in cucumber. BC1 population (189 individuals) of two inbred lines (large spine PI197088 and small spine SA0422) was used for primary mapping of the SS/ss locus with 7 markers covering an interval of 37.1cM. An F-2 segregating population of 1032 individuals constructed from the same two parents (PI197088 and SA0422) was used to fine mapping of the SS/ss locus. Six new markers linked to the gene were successfully screened for construction of a fine linkage map, in which the SS/ss locus was located in the region flanked by marker SE1 (3 recombinants) and SSR43 (2 recombinants) with a 189kb physical distance. Markers from this study will be valuable for candidate gene cloning and marker-assisted selection for cucumber breeding.
Improving the combining ability for grain quality traits of the parents is the key factor to enhance averaged bulk grain quality of hybrid japonica rice. Eight quality traits including brown rice rate, milled rice rate (MRR), head rice rate (HRR), chalkiness degree (CD), percentage of chalky grain (PCG), alkali spreading value (ASV), gel consistency (GC) and amylose content (AC) of the bulked sample of rough rice harvested from the 81 F-1 hybrid plants were investigated in 2014 and 2015. By combining the phenotypic data of general combining ability (GCA) for the quality traits with genotypic data of single nucleotide polymorphism (SNP) obtained by genotyping by sequencing method, CAScreen1.0 program compiled by MATLAB language was conducted to identify the elite SNP genotype associated with combining ability of quality traits in parents. Totally 35 elite SNP genotypes involving 22 genes (genotypes) were detected associated with GCA of seven quality traits (P<0.05) in both 2014 and 2015. Seven and four SNPs were detected associated with combining ability for MRR and HRR, respectively. For PCG and CD, six and ten SNPs were detected associated with combining ability of parents, respectively. Six SNPs involving two genes were detected for combining ability of GC. Only two SNPs were detected which associated with combining ability for ASV. For combining ability of AC, six elite SNPs genotype were detected. Among them, elite SNP genotype of LOC_Os08g25220 (T/C) located on chromosome 8 could significantly reduce AC content in mixed rice samples of hybrid japonica rice.
Both low-temperature germinability (LTG) and cold tolerance at the seedling stage (CTS) are important traits for rice. In this study, a rice population of recombinant inbred lines (RILs), derived from the backcross population of a cross between Dongnong422 and Kongyu131, was developed to detect quantitative trait loci (QTL) affecting LTG and CTS by using seed of different storage times. Correlation analysis indicated that there was no significant relationship between LTG and CTS, suggesting that cold tolerance might be genetic differences for LTG and CTS. In total, Twelve and twenty-three major QTLs were detected for LTG and CTS, respectively, which could explain greater than 10% of the phenotypical variation. Eight (qCG12-1, qGI12-1, qGV9-1, qMLIT12-1, qPV6-1, qMDG12-1, qLDW-cold10-1, qLFWcold10-1) significant QTLs were mapped for different storage time, it concluded that such QTLs were not affected by environment (storage time) and were closely related QTLs to cold tolerance. One or more QTLs were identified for each trait with some of these QTLs co-locating, qMLIT7-1, qCG7-1, and qGI7-1 for LTG, qLFWcold10-1, and qLDWcold10-1 for CTS with contributions over 15% were mapped common marker interval, respectively, co-location of QTLs for different traits can be an indication that a locus has pleiotropic effects on multiple traits due to a common mechanistic basis. Two lines, RIL128 and RIL73, might be valuable to improve the LTG and CTS through a combination of crosses. The identified QTLs might be applicable to improve the rice cold tolerance by the marker-assisted selection approach.
The timing of spring bud flush (TBF) in tea plants (Camellia sinensis) is an adaptive critical and economically important trait; thus, it has been a focus of many tea-breeding programs. Previously, we reported the mapping of two major and partial linked TBF QTLs onto the LG01 of C. sinensis using a full-sib population of 'Longjing 43' x 'Baihaozao'. In this study, we further tested the QTL stability and expression variation in different years, experimental sites, and crossing parents. We genotyped 157 additional F1 individuals from the 'Longjing 43' x 'Baihaozao' cross and 173 F1 individuals from 'Wuniuzao' x 'Longjing 43' cross with 16 and 17 SSR markers on LG01, respectively. We also recorded the TBF trait of the two populations at Hangzhou and/or Shengzhou sites in the spring of 2014, 2015 and/or 2017. The TBF QTLs were significant (P < 0.001 at the chromosome-wide level) in all tested years, sites, and populations, but the explained phenotypic variation ranged considerable (26.2-40.5%, two QTLs were considered together in the Interval Mapping). Interestingly, the QTLs only segregated in 'Longjing 43' among the three parents involved. After grouping the individuals by the genotypes of the two markers closest to the QTLs, a maximum difference of 9.22 days for the average TBF was observed between the earliest and latest groups.
To better understand the underlying mechanisms of agronomic traits related to drought resistance and discover candidate genes or chromosome segments for drought-tolerant rice breeding, a fundamental introgression population, BC3, derived from the backcross of local upland rice cv. Haogelao (donor parent) and super yield lowland rice cv. Shennong265 (recurrent parent) had been constructed before 2006. Previous quantitative trait locus (QTL) mapping results using 180 and 94 BC3F6,7 rice introgression lines (ILs) with 187 and 130 simple sequence repeat (SSR) markers for agronomy and physiology traits under drought in the field have been reported in 2009 and 2012, respectively. In this report, we conducted further QTL mapping for grain yield component traits under water-stressed (WS) and well-watered (WW) field conditions during 3 years (2012, 2013 and 2014). We used 62 SSR markers, 41 of which were newly screened, and 492 BC4F2,4 core lines derived from the fourth backcross between D123, an elite drought-tolerant IL (BC3F7), and Shennong265. Under WS conditions, a total of 19 QTLs were detected, all of which were associated with the new SSRs. Each QTL was only identified in 1 year and one site except for qPL-12-1 and qPL-5, which additively increased panicle length under drought stress. qPL-12-1 was detected in 2013 between new marker RM1337 and old marker RM3455 (34.39 cM) and was a major QTL with high reliability and 15.36% phenotypic variance. qPL-5 was a minor QTL detected in 2013 and 2014 between new marker RM5693 and old marker RM3476. Two QTLs for plant height (qPHL-3-1 and qPHP-12) were detected under both WS and WW conditions in 1 year and one site. qPHL-3-1, a major QTL from Shennong265 for decreasing plant height of leaf located on chromosome 3 between two new markers, explained 22.57% of phenotypic variation with high reliability under WS conditions. On the contrary, qPHP-12 was a minor QTL for increasing plant height of panicle from Haogelao on chromosome 12. Except for these two QTLs, all other 17 QTLs mapped under WS conditions were not mapped under WW conditions; thus, they were all related to drought tolerance. Thirteen QTLs mapped from Haogelao under WS conditions showed improved drought tolerance. However, a major QTL for delayed heading date from Shennong265, qDHD-12, enhanced drought tolerance, was located on chromosome 12 between new marker RM1337 and old marker RM3455 (11.11 cM), explained 21.84% of phenotypic variance and showed a negative additive effect (shortening delay days under WS compared with WW). Importantly, chromosome 12 was enriched with seven QTLs, five of which, including major qDHD-12, congregated near new marker RM1337. In addition, four of the seven QTLs improved drought resistance and were located between RM1337 and RM3455, including three minor QTLs from Haogelao for thousand kernel weight, tiller number and panicle length, respectively, and the major QTL qDHD-12 from Shennong265. These results strongly suggested that the newly screened RM1337 marker may be used for marker-assisted selection (MAS) in drought-tolerant rice breeding and that there is a pleiotropic gene or cluster of genes linked to drought tolerance. Another major QTL (qTKW-1-2) for increasing thousand kernel weight from Haogelao was also identified under WW conditions. These results are helpful for MAS in rice breeding and drought-resistant gene cloning.
We used Cheongcheong/Nagdong doubled haploid (CNDH) genetic map to develop early flowering furthermore heavy panicle variety. Conspicuous three lines were selected among 120 CNDH population by QTL analysis 2 years of data on CNDH heading date and panicle weight. The casein kinase I (PCKP) gene, which is related to early heading gene, was found by physical gene mapping and map-based cloning. PCKP is involved in the control of rice flowering time by modulating the day-length response. PCKP acts as an inhibitor in the rice flowering pathway by enhancing the photoperiod response. In northern part, rice is harvested on October, however rice yield is reduce due to the frequent typhoon during September. However, if the rice varieties developed in this study are used, they can be harvested with high yield before environmental disaster, which will be efficient for safely cope with food.
Interspecific hybrids between related species have long been used for transferring desirable genes, broadening genetic diversity and utilizing intersubgenomic heterosis. In this study, we developed a novel Brassica rapa type (AA, 2n = 20) exhibiting certain features derived from interspecific hybridization between natural B. rapa and Brassica juncea (AABB, 2n = 36). In pollen mother cells (PMCs) of the novel B. rapa type, normal chromosome pairing with 10 bivalents and 10: 10 segregation was observed, and the novel B. rapa lines were completely fertile. However, GISH showed that certain B chromosomes or fragments were introgressed into B. rapa. Genetic components of the novel B. rapa lines were investigated by GISH, AFLP and SSR analyses. GISH analysis of F-1, BC1F1, and BC1F2 plants confirmed the identities of three addition lines and seven translocation lines. AFLP and SSR analyses of 60 hybrid progenies from BC1F4 plants, their parents, and some B. juncea and B. rapa resources indicated that the A(J) and B chromosome(s) or fragment(s) introgressed to the novel B. rapa. AFLP revealed that 60 BC1F4 plants contained B chromosomes or fragments, which evidenced introgression into the hybrid progeny. SSR analysis indicated that the A-genome (A1-A10) of B. juncea was introgressed into the hybrid progeny at 1.0 to 42.7%. Lastly, we obtained some yellow-seed and early-flowering B. rapa resources. The novel B. rapa lines can be used to genetically improve B. rapa in the Qinghai-Tibet Plateau and to study the origin and evolution of the A- and B-genomes.
DNA methylation is a vital epigenetic modification for the regulation of plant response to environmental stresses. In order to investigate changes in DNA methylation under salt stress, the levels of cytosine methylation in maize leaves at the seedling stage were estimated using the Methylated DNA Immunoprecipitation Sequencing (MeDIP-seq) method. The profiling of the DNA methylation results showed that a total of 163.27 million raw reads were obtained, with an average 33.06% of which were uniquely mapped to a specific region in the maize genome. Cytosine methylation mainly occurred in CG, CHG, and CHH (H = A, T, or G) sites, and the CG contexts were lower than CHG and CHH contexts. The distribution of highly methylated regions (HMRs) mainly focused on the upstream 2k, intron, and downstream 2k, and the HMR distribution in these elements of YH 200 was higher than control (YH 0) and other samples. In addition, a total of 4402 differential methylated region (DMR)-associated genes were observed between stress samples and control, in which more hypomethylation-related genes were present than hypermethylation-related ones under 100 and 200 mmol L-1 NaCl stress. Meanwhile, these DMR-associated genes were found to be involved in many biological functions by gene ontology (GO) analysis, such as cellular processes, metabolic processes, and signal transduction. Real-time qRT-PCR results showed that the expression of some methylated genes was consistent with the results of MeDIP-seq, while others showed an opposite trend, indicating that DNA-methylated regions did not uniformly affect the transcription of the corresponding genes. These experimental results are expected to improve our understanding of salt tolerance in maize.
Aphid, Macrosiphoniella sanbourni, is a major insect pest that adversely affects ornamental quality and production of chrysanthemum, thus it is critical to develop new cultivars resistant to aphid. However, the genetic mechanism governing aphid resistance is thus far not thoroughly investigated in chrysanthemum. This study aimed to characterize the genetic variation of the aphid resistance in a global collection of 80 chrysanthemum entries, during summer and autumn under greenhouse condition, and to identify the molecular markers for aphid resistance by association mapping. The performances of aphid resistance, quantified by the average damage index of aphid, was significantly correlated (r = 0.93, P<0.01) between two seasons. The coefficients phenotypic and genetic variation was calculated around 26-27%; and a high magnitude (0.93) of broad-sense heritability, together with a moderate relative genetic advance (similar to 68%), was estimated for aphid resistance. By using the MLM model that integrates population structure and kinship matrix as covariates association mapping identified 11 markers related to aphid resistance, with the individually explained phenotypic variation ranging from similar to 11 to similar to 57%. Of the three markers predicted in both seasons, SSR184-1 and E1M5-1were identified as favorable alleles for aphid resistance. Seven cultivars harboring the two favorable alleles were identified as potential donor parents for future improvement of resistance against aphid. These findings add further understanding of the genetic determination of aphid resistance, and the identified favorable alleles and donor parents open a possibility to produce chrysanthemums with enhanced aphid resistance in future.
The bottleneck of microsatellite marker development is to determine polymorphisms of microsatellite markers. A large amount of microsatellites can be detected via high-throughput sequencing. However, most previous studies didn't fully use the high-throughput sequencing data to predict number of alleles at microsatellite loci. Instead, laborious experiments were performed for manually screening microsatellite loci, finding out number of alleles at each microsatellite loci and selecting those with polymorphisms for marker development. In this study, we improved the method for efficient development of polymorphic microsatellite markers from high-throughput transcriptome sequencing, using hexaploid oil-tea camellia as a case study. Leaf transcriptomes were sequenced of eight wild oil-tea camellia samples at different altitudes in Jinggang and Lu Mountains, China. Microsatellites were directly identified in the sequencing reads and primers were designed. Strategies were designed to filtering duplicate and multilocus markers. For each marker, number of alleles cross samples was predicted and length of the potentially amplifiable sequence was estimated. 153 predicted polymorphic markers were selected and empirically validated in the eight samples. Sixty five markers (42%) were polymorphic (2-12 alleles) and 31 (20%) were highly polymorphic (6-12 alleles). The empirical number of alleles was generally higher than the predicted number of alleles but they were significantly correlated. The predicted allele length was among the empirical allele length range. Compared with most previous studies, the method shows a higher efficiency for developing polymorphic markers and filtering duplicate and multi-locus markers. The polymorphic microsatellite markers developed can be used for analyzing the genetic diversity of oil-tea camellia.
Gossypium turneri, a wild cotton species (2n = 2X = 26, D10D10) originating from Mexico, possesses invaluable characteristics unavailable in the cultivated tetraploid cotton gene pool, such as caducous involucels at anthesis, resistance to insects and tolerance to abiotic stresses. However, transferring desired characteristics from wild species into cultivated cotton is often fraught with diverse obstacles. Here, Gossypium hirsutum (as the maternal parent) and G. turneri were crossed in the Hainan Province of China, and the obtained hybrid seeds (2n = 3X = 39, ADD(10)) were treated with 0.075% colchicine solution for 48 h to double the chromosome complement in order to overcome triploid F-1 sterility and to generate a fertile hexaploid. Chromosome doubling was successful in four individuals. However, the new synthetic hexaploids derived from these individuals were still highly sterile, and no seeds were generated by selfing or crossing. Therefore, an embryo rescue technique was employed in an attempt to produce progenies from the new synthetic hexaploids. Consequently, a total of six large embryos were obtained on MSB2K medium supplemented with 0.5 mg l(-1) KIN and 250 mg l(-1) CH using ovules from backcrossing that were 3 days post-anthesis. Four grafted surviving seedlings were confirmed to be the progenies (pentaploids) of the new synthetic hexaploids using cytological observations and molecular markers. Eight putative fertile individuals derived from backcrossing the above pentaploids were confirmed using SSR markers and generated an abundance of normal seeds. This research lays a foundation for transferring desirable characteristics from G. turneri into upland cotton.