In the subtribe Maydeae, Tripsacum and Zea are closely related genera. Tripsacum is a horticultural crop widely used as pasture forage. Previous studies suggested that Tripsacum might play an important role in maize origin and evolution. However, our understanding of the genomics and the evolution of Tripsacum remains limited. In this study, two diploids, T. dactyloides var. meridionale (2n = 36, MR) and T. dactyloides (2n = 36, DD), and one tetraploid, T. dactyloides (2n = 72, DL) were sequenced by low-coverage genome sequencing followed by graph-based cluster analysis. The results showed that 63.23%, 59.20%, and 61.57% of the respective genome of MR, DD, and DL were repetitive DNA sequence. The proportions of different repetitive sequences varied greatly among the three species. Fluorescence in situ hybridization (FISH) analysis of mitotic metaphase chromosomes with satellite repeats as the probes showed that the FISH signal patterns of DL were more similar to that of DD than to that of MR. Comparative analysis of the repeats also showed that DL shared more common repeat families with DD than with MR. Phylogenetic analysis of internal transcribed spacer region sequences further supported the evolutionary relationship among the three species. Repetitive sequences comparison showed that Tripsacum shared more repeat families with Zea than with Coix and Sorghum. Our study sheds new light on the genomics of Tripsacum and differential speciation in the Poaceae family.
Cotton is the world's most important natural fiber crop. It is also a model system for studying polyploidization, genomic organization, and genome-size variation. Integrating the cytological characterization of cotton with its genetic map will be essential for understanding its genome structure and evolution, as well as for performing further genetic-map based mapping and cloning. In this study, we isolated a complete set of bacterial artificial chromosome clones anchored to each of the 52 chromosome arms of the tetraploid cotton Gossypium hirsutum. Combining these with telomere and centromere markers, we constructed a standard karyotype for the G. hirsutum inbred line TM-1. We dissected the chromosome arm localizations of the 45S and 5S rDNA and suggest a centromere repositioning event in the homoeologous chromosomes AT09 and DT09. By integrating a systematic karyotype analysis with the genetic linkage map, we observed different genome sizes and chromosomal structures between the subgenomes of the tetraploid cotton and those of its diploid ancestors. Using evidence of conserved coding sequences, we suggest that the different evolutionary paths of non-coding retrotransposons account for most of the variation in size between the subgenomes of tetraploid cotton and its diploid ancestors. These results provide insights into the cotton genome and will facilitate further genome studies in G. hirsutum.
Chromosome identification and karyotype using fluorescence in situ hybridization (FISH) provides a technical platform for genome and cytogenetic studies. Brassica juncea (brown mustard, 2n = 4 × = 36; genome AABB) is an allopolyploid species that originated from a spontaneous hybridization of Brassica rapa and Brassica nigra and contains many valuable traits. In this study, a multicolor FISH procedure allowing the identification of all 18 chromosomal pairs was developed by two-step hybridizations with probes on the same metaphase chromosomes. The distribution patterns and chromosomal localizations of six repeat sequences (satellite repeat pBrSTR, 5S rDNA, 45S rDNA, B genome-specific repeat pBNBH35, and centromeric satellite repeats CentBr1 and CentBr2) on B. juncea chromosomes were characterized. Comparative karyotype analyses showed that the genome is relatively stable in comparison with its diploid progenitor species and revealed intraspecific karyotypic diversity among three accessions of B. juncea. This study provides valuable information about the genome evolution of B. juncea and a toolkit that will be helpful for chromosome identification.
Interspecific hybridization and allopolyploidization contribute to the improvement of many important crops. Recently, we successfully developed an amphidiploid from an interspecific cross between cucumber (Cucumis sativus, 2n = 2x = 14) and its relative C. hystrix (2n = 2x = 24) followed by chemical induction of chromosome doubling. The resulting allotetraploid plant was self-pollinated for three generations. The fertility and seed set of the amphidiploid plants were very low. In this study, we investigated the meiotic chromosome behavior in pollen mother cells with the aid of fluorescence in situ hybridization, aiming to identify the reasons for the low fertility and seed set in the amphidiploid plants. Homologous chromosome pairing appeared normal, but chromosome laggards were common, owing primarily to asynchronous meiosis of chromosomes from the two donor genomes. We suggest that asynchronous meiotic rhythm between the two parental genomes is the main reason for the low fertility and low seed set of the C. hystrix-cucumber amphidiploid plants.
Iron and zinc are two trace elements that are essential for rice. But they are toxic at higher concentrations, leading to severe rice yield losses especially in acid soils and inland valleys. In this study, two reciprocal introgression line (IL) populations sharing the same parents were used with high-density SNP bin markers to identify QTL tolerant to iron and zinc toxicities. The results indicated that the japonica variety 02,428 had stronger tolerance to iron and zinc toxicities than the indica variety Minghui 63. Nine and ten QTL contributing to iron and zinc toxicity tolerances, respectively, were identified in the two IL populations. The favorable alleles of most QTL came from 02,428. Among them, qFRRDW2, qZRRDW3, and qFRSDW11 appeared to be independent of genetic background. The region C11S49-C11S60 on chromosome 11 harbored QTL affecting multiple iron and zinc toxicity tolerance-related traits, indicating partial genetic overlap between the two toxicity tolerances. Our results provide essential information and materials for developing excellent rice cultivars with iron and/or zinc tolerance by marker-assisted selection (MAS).
Flax is an important economic crop for seed oil and stem fiber. Phenotyping of traits such as seed yield, seed quality, stem fiber yield, and quality characteristics is expensive and time consuming. Genomic selection (GS) refers to a breeding approach aimed at selecting preferred individuals based on genomic estimated breeding values predicted by a statistical model based on the relationship between phenotypes and genome-wide genetic markers. We evaluated the prediction accuracy of GS (rMP) and the efficiency of GS relative to phenotypic selection (RE) for three GS models: ridge regression best linear unbiased prediction (RR-BLUP), Bayesian LASSO (BL), and Bayesian ridge regression (BRR), for seed yield, oil content, iodine value, linoleic, and linolenic acid content with a full and a common set of genome-wide simple sequence repeat markers in each of three biparental populations. The three GS models generated similar rMP and RE, while BRR displayed a higher coefficient of determination (R2) of the fitted models than did RR-BLUP or BL. The mean rMP and RE varied for traits with different heritabilities and was affected by the genetic variation of the traits in the populations. GS for seed yield generated a mean RE of 1.52 across populations and marker sets, a value significantly superior to that for direct phenotypic selection. Our empirical results provide the first validation of GS in flax and demonstrate that GS could increase genetic gain per unit time for linseed breeding. Further studies for selection of training populations and markers are warranted.
Tea is an important cash crop, representing a $40 billion-a-year global market. Differentiation of the tea market has resulted in increasing demand for tea products that are sustainably and responsibly produced. Tea authentication is important because of growing concerns about fraud involving premium tea products. Analytical technologies are needed for protection and value enhancement of high-quality brands. For loose-leaf teas, the challenge is that the authentication needs to be established on the basis of a single leaf, so that the products can be traced back to the original varieties. A new generation of molecular markers offers an ideal solution for authentication of processed agricultural products. Using a nanofluidic array to identify variant SNP sequences, we tested genetic identities using DNA extracted from single leaves of 14 processed commercial tea products. Based on the profiles of 60 SNP markers, the genetic identity of each tea sample was unambiguously identified by multilocus matching and ordination analysis. Results for repeated samples of multiple tea leaves from the same products (using three independent DNA extractions) showed 100% concordance, showing that the nanofluidic system is a reliable platform for generating tea DNA fingerprints with high accuracy. The method worked well on green, oolong, and black teas, and can handle a large number of samples in a short period of time. It is robust and cost-effective, thus showing high potential for practical application in the value chain of the tea industry.
Yellow maize contains high levels of β-carotene (βC), making it an important crop for combating vitamin A deficiency through biofortification. In this study, nine maize inbred lines were selected at random from 31 provitamin A (PVA) maize inbred lines and crossed in a partial diallel mating design to develop 36 crosses. The crosses were evaluated in the field in two locations (Samaru and Kerawa) and their seed carotenoid content were determined by high-performance liquid chromatography. The modes of gene action, heritability, and correlations between agronomic traits and carotenoid content were estimated. Additive genetic variances (σ2a) were lower than non-additive genetic variances (σ2d) for all the carotenoids, plant height (PH), and grain yield (GY), suggesting a preponderance of non-additive gene action. Broad-sense heritability (H2) was high (H2 > 60%) for zeaxanthin, days to anthesis, and PH, moderate (30% < H2 < 60%) for lutein and GY, and low (H2 < 30%) for alpha carotene, beta cryptoxanthin, βC, and PVA. Genetic advance as a percentage of mean, considered with H2,22, also suggests a preponderance of non-additive gene action for PVA carotenoids. Hybrid variety development is thus an appropriate approach to improving grain yield and PVA. GY showed no significant genotypic correlations with carotenoid content, suggesting that these traits can be improved concurrently. Thus, there is ample scope for improvement of PVA and GY in the sample of tropical-adapted maize.
Soil alkali-hydrolyzable nitrogen, which is sensitive to N fertilization rate, is one of the indicators of soil nitrogen supplying capacity. Two field experiments were conducted in Dongtai (120°19″ E, 32°52″ N), Jiangsu, China in 2009 and Dafeng (120°28″ E, 33°12″ N), Jiangsu province, China in 2010. Six nitrogen rates (0, 150, 300, 375, 450, and 600 kg ha− 1) were used to study the effect of N fertilization rate on soil alkali-hydrolyzable nitrogen content (SAHNC), subtending leaf nitrogen concentration (SLNC), yield, and fiber quality. In both Dongtai and Dafeng experiment station, the highest yield (1709 kg ha− 1), best quality (fiber length 30.6 mm, fiber strength 31.6 cN tex− 1, micronaire 4.82), and highest N agronomic efficiency (2.03 kg kg− 1) were achieved at the nitrogen fertilization rate of 375 kg ha− 1. The dynamics of SAHNC and SLNC could be simulated with a cubic and an exponential function, respectively. The changes in SAHNC were consistent with the changes in SLNC. Optimal average rate (0.276 mg day− 1) and duration (51.8 days) of SAHNC rapid decline were similar to the values obtained at the nitrogen rate of 375 kg ha− 1 at which cotton showed highest fiber yield, quality, and N agronomic efficiency. Thus, the levels and strategies of nitrogen fertilization can affect SAHNC dynamics. The N fertilization rate that optimizes soil alkali-hydrolyzable nitrogen content would optimize the subtending leaf nitrogen concentration and thereby increase the yield and quality of the cotton fiber.
To identify a strategy for earlier sowing and harvesting of spring maize (Zea mays L.) in an alternative maize-maize double cropping system, a 2-year field experiment was performed at Quzhou experimental station of China Agricultural University in 2014 and 2015. A short-season cultivar, Demeiya number 1 (KX7349), was used in the experiment. Soil temperature to 5 cm depth in the early crop growth stage, crop growth, crop yield, and water use of different treatments (plastic film-mulched raised bed (RF) and flat field without plastic film mulching (CK) in 2014; RF, plastic film-mulched flat field (FF), and CK in 2015) were measured or calculated and compared. Soil temperature in the film-mulched treatments was consistently higher than that in CK (1.6-3.5 °C in average) during the early growth stage. Crops in plastic film-mulched treatments used 214 fewer growing-degree days (GDDs) in 2014 and 262 fewer GDDs in 2015. In 2014, the RF treatment yielded 32.7% higher biomass than CK, although its 9.4% higher grain yield was not statistically significant. Also, RF used 17.9% less water and showed 33.1% higher water use efficiency (WUE) than CK. In 2015, RF and FF showed 56.2% and 49.5% higher yield, 15.0% and 4.5% lower water use (ET), and 63.4% and 75.7% higher WUE, respectively, than CK. RF markedly increased soil temperature in the early crop season, accelerated crop growth, reduced ET, and greatly increased crop yield and WUE. Compared with FF, RF had no obvious effect on crop growth rate, although soil temperature during the period between sowing and stem elongation was slightly increased. However, RF resulted in lower ET and higher WUE than FF. Effects of RF on soil water dynamics as well as its cost-effectiveness remain topics for further study.
