Editorial: Interspecific Hybridization in Plant Biology

Many crop gene pools are derived from small numbers of founders. As a consequence of long histories of strong directional selection, crop gene pools have narrow genetic diversity available to provide inherent solutions to changing needs or challenges. Notoriously, plants can mate across taxonomically-determined species boundaries, and interspecific hybridization is widely used in plant genetics research. Interspecific hybridizations have conferred practical improvements to crops, some of which are unexpected based on the phenotypes of the parents. Genomics has provided insights into the fundamental consequences of interspecific hybridization for plant biology. Additionally, genomics has allowed the development of molecular tools for dissecting the genetic control of phenotypic variation in interspecific hybrid populations and manipulating interspecific introgressions in crop improvement. This Research Topic aimed to publish peer-reviewed research in plant interspecific hybridization and its consequences, both fundamental and applied. While such work is prominent in plants, consideration will also be given to salient work in other taxa. A key threshold for publication was the extent to which findings are of cross-cutting interest and importance, i.e., not only to those working on the target taxon but also to a wide range of biological scientists. As a result, 15 articles were published. For the issue of the role of interspecific hybridization, Wong et al. used the genus Senecio, and revealed some of the roles interspecific hybridization could play in evolution, including transcriptome shock, genome reorganization, change in mating system and reproductive traits, and adaptive introgression. Other aspects, such as the evolution of novel compounds, gene redundancy, and the extent of adaptive allele sharing, have been explored in other Senecio species. For cultivated species, Zhou et al. highlighted the important role that interspecific hybridization-introgression has played in improving the genetic diversity and adaptation of Oryza sativa. Natural hybridization-introgression is thought to have led to the origin of indica, aus, and basmatic subgroups, which adapted to changing cultivated environments, and produced feral weedy rice coexisting and competing with cultivars under production management. Artificial interspecific hybridization-introgression gained several breakthroughs in rice breeding, such as developing three-line hybrid rice, new rice for Africa (NERICA), and deploying some important pest and disease resistance genes in rice genetic improvement, contributing to the stable increase of rice production to meet the expanding human population. For the issue of interspecific hybridization for breeding, Zhang et al. raised 6,372 agronomic trait introgression lines (ILs) from BC2 to BC6 based on the variations in agronomic traits by crossing 170 accessions of 7 AA genome species and 160 upland rice accessions of O. sativa as the donor parents, with three elite cultivars of O. sativa, Dianjingyou 1 (a japonica variety), Yundao 1 (a japonica variety), and RD23 (an indica variety) as the recurrent parents, respectively. Agronomic traits such as spreading panicle, erect panicle, dense panicle, lax panicle, awn, prostrate growth, plant height, pericarp color, kernel color, glabrous hull, grain size, 1,000-grain weight, drought resistance, and aerobic adaption, and blast resistance, were derived from more than one species. This agronomic trait introgression library from multiple species and accessions provided a powerful resource for future rice improvement and genetic dissection of agronomic traits. Tan et al. reconstructed the high-SER (stigma exsertion rate) trait based upon eighteen quantitative trait loci (QTLs) for SER from O. sativa, O. glaberrima, and O. glumaepatula using single-segment substitution lines (SSSLs) in the genetic background of Huajingxian 74 (HJX74). A total of 29 pyramiding lines with 2-6 QTLs were developed from 10 SSSLs carrying QTLs for SER in the HJX74 genetic background. The results showed that the SER increased with increasing QTLs in the pyramiding lines. The SER in the lines with 5-6 QTLs was as high as wild rice with strong outcrossing ability. Limbalkar et al. used Brassica carinata-derived lines (CDLs) in Brassica juncea (L.) Czern. background, carrying genomic segments from B. carinata, to raise 105 hybrids developed from intermating 15 CDLs in half diallel fashion. The results indicated that higher productivity under drought conditions can be realized through the development of hybrids. Ullah et al. used Trifolium occidentale, one of the ancestral parents of T. repens, as a bridging species to overcome the interspecific barrier between T. ambiguum and T. repens. Recombinant chromosome segments from T. ambiguum were found in all five plants of T. repens background. Despite early chromosome imbalances, the backcross populations were fertile and produced large numbers of seeds. These hybrids represent a major new resource for the breeding of novel resilient forms of white clover. Reproductive barriers, important in the wild to maintain species integrity, are a major obstacle to interspecific hybridization and gene introgression. Interactive RNA sequencing and proteome analysis by Du et al. revealed changes in the transcriptomic and proteomic profiles of Fragaria viridis styles harvested at 0 and 24 h after self-pollination. Differentially expressed genes and differentially abundant proteins associated with self-incompatible pollination were further mined, and multiple pathways were found to be involved. Moriyama et al. made a sibling cross of F1 plants made from the cross between Lilium × formolongi cv. Hatsuki and cv. Raizan 2go, producing the pollen-sterile line, PL01. Using PL01 and its progeny, genetic analysis suggested that the male-sterile phenotype is attributed to one recessive locus LflflTDF1. A transcript expressed only in pollen-fertile plants was homologous to TDF1 (DEFECTIVE in TAPETAL DEVELOPMENT and FUNCTION1) in Arabidopsis, a gene encoding a transcription factor AtMYB35 known as a key regulator of pollen development. The LflflTDF1 allele was transferred to Easter lily to confer sterility. He et al. reported that an imbalance in parental genomes or endosperm balance number (EBN) causes hybrid seed lethality and ovary abscission in both interspecific and intraspecific-interploidy crosses in the genus Nicotiana. Interesting, Kopecky et al. demonstrated that in Allium cepa × A. roylei hybrids, chromosomes of A. cepa are frequently substituted by those of A. roylei and in just one generation, the genomic constitution shifts from 8 A. cepa + 8 A. roylei chromosomes in the F1 generation to the average of 6.7 A. cepa + 9.3 A. roylei chromosomes in the F2 generation, inferring that female meiotic drive is the key factor underlying A. roylei genome dominance. Salina et al. identified regions of recombination suppression in wheat chromosome 5B based on comparisons of the 5B map of a cross between the Chinese Spring (CS) variety of hexaploid wheat and CS-5Bdic with several 5B maps of tetraploid and hexaploid wheat. Pan et al. reported that wheat- Agropyron cristatum derivative II-11-1 was proven to contain a pair of 5P chromosomes and a pair of 2P chromosomes with 42 wheat chromosomes by analyzing the fluorescence in situ hybridization (FISH) and expressed sequence tag (EST) markers. Additionally, cytological identification and field investigation showed that the 5P chromosome can weaken the homologous pairing of wheat chromosomes and promote pairing between homoeologous chromosomes. This provides new materials for studying the mechanism of the alien gene affecting homologous chromosome pairing and promoting homoeologous pairing of wheat. The major issue is genomics of interspecific hybrids and hybrid heterosis. Mo et al. made a comprehensive comparative transcriptome sequencing analysis of root samples from the hybrid G70 × GDH11 and its parental inbred lines G70 and GDH11 to elucidate the importance of the root uptake capacity of K+ in the formation of heterosis in Nicotiana tabacum L. The results showed that 29.53% and 60.49% of the differentially expressed genes (DEGs) exhibited dominant and over-dominant expression patterns, respectively. Li et al. applied the reciprocal interspecific hybrids and their parents (Gossypium hirsutum and Gossypium barbadense) to elucidate the transcription regulatory mechanism of early biomass heterosis. Comparative transcriptome analysis showed that transgressive down-regulation (TDR) is the main gene expression pattern in the hybrids (G. hirsutum × G. barbadense, HB). Transgressive up-regulation (TUR) is the major primary gene expression pattern in the hybrids (G. barbadense × G. hirsutum, BH). The above results demonstrated that overdominance mediates biomass heterosis in interspecific hybrid cotton and the supervisory mechanism divergence of hybrids with different females. Cardoso-Silva et al. identified and characterized Orphan genes (OGs) in sugarcane. The results obtained suggested that sugarcane OGs are involved in several biological mechanisms, including stimulus response and defense mechanisms. In summary, the research collected on this topic facilitated understanding of issues related to interspecific hybridization in plant biology. We believe that this platform for enhancing exchange and promoting development has merit to be continued regarding some issues such as genomics of natural or synthetic polyploid formation, genomic responses to interspecific hybridization, transmission genetics across species boundaries, and genomics of interspecific hybrid heterosis.Non peer reviewe

Identification of a Drosophila Vitamin K-dependent γ-Glutamyl Carboxylase

Using reduced vitamin K, oxygen, and carbon dioxide, gamma-glutamyl carboxylase post-translationally modifies certain glutamates by adding carbon dioxide to the gamma position of those amino acids. In vertebrates, the modification of glutamate residues of target proteins is facilitated by an interaction between a propeptide present on target proteins and the gamma-glutamyl carboxylase. Previously, the gastropod Conus was the only known invertebrate with a demonstrated vitamin K-dependent carboxylase. We report here the discovery of a gamma-glutamyl carboxylase in Drosophila. This Drosophila enzyme is remarkably similar in amino acid sequence to the known mammalian carboxylases; it has 33% sequence identity and 45% sequence similarity to human gamma-glutamyl carboxylase. The Drosophila carboxylase is vitamin K-dependent, and it has a K(m) toward a model pentapeptide substrate, FLEEL, of about 4 mm. However, unlike the human gamma-glutamyl carboxylase, it is not stimulated by human blood coagulation factor IX propeptides. We found the mRNA for Drosophila gamma-glutamyl carboxylase in virtually every embryonic and adult stage that we investigated, with the highest concentration evident in the adult head

Cytoplasm affects grain weight and filled-grain ratio in indica rice

<p>Abstract</p> <p>Background</p> <p>Cytoplasmic effects on agronomic traits -involving cytoplasmic and nuclear genomes of either different species or different cultivars - are well documented in wheat but have seldom been demonstrated in rice (<it>Oryza sativa </it>L.). To detect cytoplasmic effects, we introgressed the nuclear genomes of three <it>indica </it>cultivars - Guichao 2, Jiangchengkugu, and Dianrui 449 - into the cytoplasms of six <it>indica </it>cultivars - Dijiaowujian, Shenglixian, Zhuzhan, Nantehao, Aizizhan, and Peta. These 18 nuclear substitution lines were evaluated during the winter season of 2005 in Sanya, Hainan, China, and during the summer season of 2006 in Kunming, Yunnan, China. The effects of 6 cytoplasm sources, 3 nucleus sources, 2 locations and their interactions were estimated for plant height, panicle length, panicle number per plant, spikelet number per panicle, grain weight, filled-grain ratio, and yield per plot.</p> <p>Results</p> <p>For five of the seven traits, analysis of variance showed that there were no significant cytoplasmic effects or interactions involving cytoplasmic effects. The effect of cytoplasm on 1000-grain weight was highly significant. Mean 1000-grain weight over the two locations in four of the six cytoplasms clustered close to the overall mean, whereas plants with Nantehao cytoplasm had a high, and those with Peta cytoplasm a low mean grain weight. There was a highly significant three-way interaction affecting filled-grain ratio. At Sanya, cytoplasms varied in very narrow ranges within nuclear backgrounds. Strong cytoplasmic effects were observed only at Kunming and in only two of the three nuclear backgrounds; in the Jianchenkugu nuclear background, there was no evidence of strong cytoplasmic effects at either location. In the Dianrui 449 and Guichao 2 nuclear background evaluated at Kunming, filled-grain ratios of the six cytoplasms showed striking rank shifts</p> <p>Conclusions</p> <p>We detected cytoplasmic variation for two agronomically important traits in <it>indica </it>rice. The cytoplasm source had a significant effect on grain weight across the two experimental locations. There was also a significant cytoplasmic effect on filled-grain ratio, but only in two of three nuclear background and at one of the two locations. The results extend our previous findings with <it>japonica </it>rice, suggesting that the selection of appropriate cytoplasmic germplasm is broadly important in rice breeding, and that cytoplasmic effects on some traits, such as filled-grain ratio, cannot be generalized; effects should be evaluated in the nuclear backgrounds of interest and at multiple locations.</p

Identification of rhizome-specific genes by genome-wide differential expression Analysis in Oryza longistaminata

<p>Abstract</p> <p>Background</p> <p>Rhizomatousness is a key component of perenniality of many grasses that contribute to competitiveness and invasiveness of many noxious grass weeds, but can potentially be used to develop perennial cereal crops for sustainable farmers in hilly areas of tropical Asia. <it>Oryza longistaminata</it>, a perennial wild rice with strong rhizomes, has been used as the model species for genetic and molecular dissection of rhizome development and in breeding efforts to transfer rhizome-related traits into annual rice species. In this study, an effort was taken to get insights into the genes and molecular mechanisms underlying the rhizomatous trait in <it>O. longistaminata </it>by comparative analysis of the genome-wide tissue-specific gene expression patterns of five different tissues of <it>O. longistaminata </it>using the Affymetrix GeneChip Rice Genome Array.</p> <p>Results</p> <p>A total of 2,566 tissue-specific genes were identified in five different tissues of <it>O. longistaminata</it>, including 58 and 61 unique genes that were specifically expressed in the rhizome tips (RT) and internodes (RI), respectively. In addition, 162 genes were up-regulated and 261 genes were down-regulated in RT compared to the shoot tips. Six distinct <it>cis</it>-regulatory elements (CGACG, GCCGCC, GAGAC, AACGG, CATGCA, and TAAAG) were found to be significantly more abundant in the promoter regions of genes differentially expressed in RT than in the promoter regions of genes uniformly expressed in all other tissues. Many of the RT and/or RI specifically or differentially expressed genes were located in the QTL regions associated with rhizome expression, rhizome abundance and rhizome growth-related traits in <it>O. longistaminata </it>and thus are good candidate genes for these QTLs.</p> <p>Conclusion</p> <p>The initiation and development of the rhizomatous trait in <it>O. longistaminata </it>are controlled by very complex gene networks involving several plant hormones and regulatory genes, different members of gene families showing tissue specificity and their regulated pathways. Auxin/IAA appears to act as a negative regulator in rhizome development, while GA acts as the activator in rhizome development. Co-localization of the genes specifically expressed in rhizome tips and rhizome internodes with the QTLs for rhizome traits identified a large set of candidate genes for rhizome initiation and development in rice for further confirmation.</p

Mapping and breeding value evaluation of a semi-dominant semi-dwarf gene in upland rice

Plant height is an important trait related to yield potential and plant architecture. A suitable plant height plays a crucial role in improvement of rice yield and lodging resistance. In this study, we found that the traditional upland landrace ‘Kaowenghan’ (KWH) showed a special semi-dwarf phenotype. To identify the semi-dwarf gene from KWH, we raised BC2F4 semi-dwarf introgression lines (IL) by hybridization of the japonica rice cultivar ‘Dianjingyou1’ (DJY1) and KWH in a DJY1 background. The plant height of the homozygous semi-dwarf IL (IL-87) was significantly reduced compared with that of DJY1. The phenotype of the F1 progeny of the semi-dwarf IL-87 and DJY1 showed that the semi-dwarf phenotype was semi-dominant. QTL mapping indicated that the semi-dwarf phenotype was controlled by a major QTL qDH1 and was localized between the markers RM6696 and RM12047 on chromosome 1. We also developed near-isogenic lines (NIL) from the BC3F3 population, and found that the yield of homozygous NIL (NIL-2) was not significantly different compared to DJY1. Breeding value evaluation through investigation of the plant height of the progeny of NIL (NIL-2) and cultivars from different genetic background indicate that the novel semi-dwarf gene shows potential as a genetic resource for rice breeding. Keywords: Semi-dwarf, QTL mapping, Breeding value evaluatio

The impact of agricultural technology adoption on income inequality in rural China: Evidence from southern Yunnan Province

This study analyzes the impact on income inequality of government efforts to increase agricultural incomes in rural China. It collects and analyzes survey data from 473 households in Yunnan, China in 2004. In particular, it investigates the effects of government efforts to promote improved upland rice technologies. Our analysis shows that farmers who adopted these technologies had incomes approximately 15% higher than non-adopters. Despite this relatively large increase, we estimate that the impact on income inequality was relatively slight. This is primarily due to the fact that lower-income farmers adopted the improved rice technology at rates that were roughly equivalent to those of higher-income farmers.Rural economic development Chinese economic development Upland rice Income inequality Agricultural income policy