Superior japonica rice variety YJ144 with improved rice blast resistance, yield, and quality achieved using molecular design and multiple breeding strategies.
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ABSTRACT: Supplementary information
The online version contains supplementary material available at 10.1007/s11032-021-01259-4.
SUBMITTER: Mao T
PROVIDER: S-EPMC8498087 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:BackgroundBalancing the yield, quality and resistance to disease is a daunting challenge in crop breeding due to the negative relationship among these traits. Large-scale genomic landscape analysis of germplasm resources is considered to be an efficient approach to dissect the genetic basis of the complex traits. Central China is one of the main regions where the japonica rice is produced. However, dozens of high-yield rice varieties in this region still exist with low quality or susceptibility to blast disease, severely limiting their application in rice production.ResultsHere, we re-sequence 200 japonica rice varieties grown in central China over the past 30 years and analyze the genetic structure of these cultivars using 2.4 million polymorphic SNP markers. Genome-wide association mapping and selection scans indicate that strong selection for high-yield and taste quality associated with low-amylose content may have led to the loss of resistance to the rice blast fungus Magnaporthe oryzae. By extensive bioinformatic analyses of yield components, resistance to rice blast, and taste quality, we identify several superior alleles for these traits in the population. Based on this information, we successfully introduce excellent taste quality and blast-resistant alleles into the background of two high-yield cultivars and develop two elite lines, XY99 and JXY1, with excellent taste, high yield, and broad-spectrum of blast resistance.ConclusionsThis is the first large-scale genomic landscape analysis of japonica rice varieties grown in central China and we demonstrate a balancing of multiple agronomic traits by genomic-based strategy.
| S-EPMC8493723 | biostudies-literature
Project description:Japonica rice mainly distributes in north of China, which accounts for more than half of the total japonica rice cultivated area of China. High yield, good grain quality and early heading date were the main breeding traits and commercial property in this region. We performed re-sequencing and genome wide variation analysis of one typical northern japonica rice variety Longdao24 and its parents (Longdao5 and Jigeng83) using the Illumina sequencing technology. 53.17 G clean bases were generated and more than 96.8% of the reads were mapped to the genomic reference sequence. An overall average effective depth of 43.67 × coverage was achieved. We identified 420,475 SNPs, 95,624 InDels, and 14,112 SVs in Longdao24 genome with the genomic sequence of the japonica cultivar Nipponbare as reference. We identified 361,117 SNPs and 81,488 InDels between Longdao24 genome and Longdao5 genome. We also detected 428,908 SNPs and 97,209 InDels between Longdao24 genome and Jigeng83 genome. Twenty-two yield related genes, twenty-two grain quality related genes and thirty-nine heading date genes were analyzed in Longdao24. The alleles of Gn1a, EP3, SCM2, Wx, ALK, OsLF and Hd17 came from the female parent Longdao5. The other alleles of qGW8, SSIVa, SBE3, SSIIIb, SSIIc, DTH2, Ehd3 and OsMADS56 came from the male parent Jigeng83. These results will help us to research the genetics basis of yield, grain quality and early heading date in northern rice of China.
| S-EPMC5513431 | biostudies-other
Project description:BACKGROUND:Rice blast caused by Magnaporthe oryzae is the most devastating disease in rice production. Compared with seedling blast, panicle blast is considered to be more destructive, which can occur without being preceded by severe seedling blast. However, panicle blast resistance research is rarely reported. RESULTS:Bodao, a japonica landrace from Taihu Lake region, showed a high level of panicle blast resistance. In this study, a mapping population of 212 recombination inbreeding lines (RILs) was developed from a cross of Bodao and the susceptible cultivar Suyunuo, and the RILs were evaluated for panicle blast resistance in three trials. Two quantitative trait loci (QTLs) qPb11-1 and qPb6-1 for panicle-blast resistance were identified, including a major QTL qPb11-1 (Pb-bd1) on chromosome 11 of Bodao explaining from 55.31% to 71.68% of the phenotype variance, and a minor QTL qPb6-1 on chromosome 6 of Suyunuo explaining from 3.54% to 6.98% of the phenotype variance. With the various segregation populations, Pb-bd1 was fine mapped in a 40.6 Kb region flanked by markers BS83 and BS98, and six candidate genes were identified within this region, including one gene encoding NAC domain-containing protein, one gene encoding unknown expression proteins, two genes encoding nucleotide binding site-leucine rich repeat (NBS-LRR) type disease resistance proteins, and two genes encoding von Willebrand factor type A (VWA) domain containing proteins. For application in rice breeding, three introgression lines of Pb-bd1with significantly enhanced panicle blast resistance were developed by using molecular assisted method (MAS) from the commercial variety Nanjing46 (NJ46). CONCLUSION:Two QTLs, qPb11-1(Pb-bd1) and qPb6-1 conferring panicle blast resistance, were identified from japonica landrace Bodao and Suyunuo.qPb11-1(Pb-bd1) was fine mapped in a 40.6 Kb region flanked by marker BS83 and BS98. Three introgression lines of Pb-bd1with significantly enhanced panicle blast resistance were developed by MAS method from the commercial variety NJ46. It indicated that Pb-bd1 would be useful gene source in panicle blast resistance breeding.
| S-EPMC6434012 | biostudies-literature
Project description:Rice blast, caused by the fungal pathogen Magnaporthe oryzae, is a major constraint to rice production worldwide. In this study, we developed monogenic near-isogenic lines (NILs) NIL Pi9, NIL Pizt , and NIL Pi54 carrying genes Pi9, Pizt, and Pi54, respectively, by marker assisted backcross breeding using 07GY31 as the japonica genetic background with good agronomic traits. Polygene pyramid lines (PPLs) PPL Pi9+Pi54 combining Pi9 with Pi54, and PPL Pizt+Pi54 combining Pizt with Pi54 were then developed using corresponding NILs with genetic background recovery rates of more than 97%. Compared to 07GY31, the above NILs and PPLs exhibited significantly enhanced resistance frequencies (RFs) for both leaf and panicle blasts. RFs of both PPLs for leaf blast were somewhat higher than those of their own parental NILs, respectively, and PPL Pizt+Pi54 exhibited higher RF for panicle blast than NIL Pizt and NIL Pi54 (P < 0.001), hinting an additive effect on the resistance. However, PPL Pi9+Pi54 exhibited lower RF for panicle blast than NIL Pi9 (P < 0.001), failing to realize an additive effect. PPL Pizt+Pi54 showed higher resistant level for panicle blast and better additive effects on the resistance than PPL Pi9+Pi54. It was suggested that major R genes interacted with each other in a way more complex than additive effect in determining panicle blast resistance levels. Genotyping by sequencing analysis and extreme-phenotype genome-wide association study further confirmed the above results. Moreover, data showed that pyramiding multiple resistance genes did not affect the performance of basic agronomic traits. So the way to enhance levels of leaf and panicle blast resistances for rice breeding in this study is effective and may serve as a reference for breeders. Key Message: Resistant levels of rice blast is resulted from different combinations of major R genes, PPL Pizt+Pi54 showed higher resistant level and better additive effects on the panicle blast resistance than PPL Pi9+Pi54.
| S-EPMC5206849 | biostudies-literature
Project description:BACKGROUND:Flowering time, which is often associated with the length of the growth period in rice, determines the adaptability of a plant to various environments. However, little is known about how flowering-time genes affect panicle development and yield formation potential in rice after inducing the transition from vegetative growth to reproductive growth. RESULTS:To explore the relationship between floral induction and yield formation and the molecular mechanism of panicle development in rice, a novel mutant, ghd10, was identified from japonica variety Wuyunjing 7 plants subjected to ethyl methane sulfonate (EMS) treatment. The ghd10 mutant exhibited delayed flowering time, tall stalks and increased panicle length and primary branch number. Map-based cloning revealed that Ghd10 encodes a transcription factor with Cys-2/His-2-type zinc finger motifs. Ghd10 is orthologous to INDETERMINATE1 (ID1), which promotes flowering in maize (Zea mays) and is identical to the previously cloned genes Rice Indeterminate1 (RID1), Early heading date2 (Ehd2) and OsId1. Transient expression analysis of the Ghd10-GFP fusion protein in tobacco mesophyll cells showed that this protein is expressed in the nucleus. Ghd10 mRNA accumulated most abundantly in developing leaves and panicle structures, but rarely in roots. Expression analysis revealed that the expression levels of Ehd1, Hd1, RFT1, Hd3a and OsMADS15 decreased dramatically under both short-day and long-day conditions in ghd10. CONCLUSION:These results indicate that Ghd10, which encodes a promoter of flowering, influences plant height and panicle development by regulating the expression levels of some flowering-related genes, such as Ehd1, Hd1, OsMADS15 and others. The ghd10 allele is a useful resource for improvement of panicle traits in rice grown in tropical and low-latitude areas.
| S-EPMC4883695 | biostudies-literature
Project description:Grain size, one of the important components determining grain yield in rice, is controlled by the multiple quantitative trait loci (QTLs). Intensive artificial selection for grain size during domestication is evidenced in modern cultivars compared to their wild relatives. Here, we report the molecular cloning and characterization of OsLG3b, a QTL for grain length in tropical japonica rice that encodes MADS-box transcription factor 1 (OsMADS1). Six SNPs in the OsLG3b region led to alternative splicing, which were associated with grain length in an association analysis of candidate region. Quantitative PCR analysis indicated that OsLG3b expression was higher during the panicle and seed development stages. Analysis of haplotypes and introgression regions revealed that the long-grain allele of OsLG3b might have arisen after domestication of tropical japonica and spread to subspecies indica or temperate japonica by natural crossing and artificial selection. OsLG3b is therefore a target of human selection for adaptation to tropical regions during domestication and/or improvement of rice. Phylogenetic analysis and pedigree records showed that OsLG3b had been employed by breeders, but the gene still has much breeding potential for increasing grain length in indica. These findings will not only aid efforts to elucidate the molecular basis of grain development and domestication, but also facilitate the genetic improvement of rice yield.
| S-EPMC6097128 | biostudies-literature
Project description:Rice production is affected by many biotic and abiotic stresses; among them, bacterial blight (BB) and blast diseases and low soil phosphorous stress cause significant yield losses. The present study was carried out with the objective of combining the BB resistance gene, Xa21, the blast resistance gene, Pi54, and the low soil phosphorous tolerance QTL/gene, Pup1, into the genetic background of the Indian mega-rice variety, MTU1010 (Cottondora Sannalu), through marker-assisted pedigree breeding. RP5973-20-9-8-24-12-7 [a near isogenic line (NIL) of MTU1010 possessing Pup1] and RP6132 [a NIL of Akshayadhan possessing Xa21 + Pi54] were crossed and 'true' F1s were identified, using the target gene-specific markers and selfed. F2 plants, which are homozygous for all the three target genes/QTLs, were identified using PCR based markers and were advanced further through the pedigree method of breeding, with selection based on phenotypic traits specific for MTU1010. At the F5 generation, a set of 15 promising triple positive homozygous lines were identified and screened for their resistance against BB and blast diseases and tolerance to low soil P. Among them, two lines (LPK 30-18-16 and LPK 49-15-22) showed higher yields as compared to MTU1010, along with the desirable long slender grain type in both low soil P and normal soil P plots, and also exhibited high levels of resistance against BB and blast diseases, with lesser grain shattering as compared to MTU1010. These lines are being advanced for multi-location trials for validating their performance.
| S-EPMC8803164 | biostudies-literature
Project description:Key messageConsiderable breeding progress in cereal and disease resistances, but not in stem stability was found. Ageing effects decreased yield and increased disease susceptibility indicating that new varieties are constantly needed. Plant breeding and improved crop management generated considerable progress in cereal performance over the last decades. Climate change, as well as the political and social demand for more environmentally friendly production, require ongoing breeding progress. This study quantified long-term trends for breeding progress and ageing effects of yield, yield-related traits, and disease resistance traits from German variety trials for five cereal crops with a broad spectrum of genotypes. The varieties were grown over a wide range of environmental conditions during 1988-2019 under two intensity levels, without (I1) and with (I2) fungicides and growth regulators. Breeding progress regarding yield increase was the highest in winter barley followed by winter rye hybrid and the lowest in winter rye population varieties. Yield gaps between I2 and I1 widened for barleys, while they shrank for the other crops. A notable decrease in stem stability became apparent in I1 in most crops, while for diseases generally a decrasing susceptibility was found, especially for mildew, brown rust, scald, and dwarf leaf rust. The reduction in disease susceptibility in I2 (treated) was considerably higher than in I1. Our results revealed that yield performance and disease resistance of varieties were subject to considerable ageing effects, reducing yield and increasing disease susceptibility. Nevertheless, we quantified notable achievements in breeding progress for most disease resistances. This study indicated an urgent and continues need for new improved varieties, not only to combat ageing effects and generate higher yield potential, but also to offset future reduction in plant protection intensity.
| S-EPMC8580907 | biostudies-literature
Project description:BackgroundRice blast, caused by the fungus Pyricularia oryzae, represents the most damaging fungal disease of rice worldwide. Utilization of rice resistant cultivars represents a practical way to control the disease. Most of the rice varieties cultivated in Europe and several other temperate regions are severely depleted of blast resistance genes, making the identification of resistant sources in genetic background adapted to temperate environments a priority. Given these assumptions, a Genome Wide Association Study (GWAS) for rice blast resistance was undertaken using a panel of 311 temperate/tropical japonica and indica accessions adapted to temperate conditions and genotyped with 37,423 SNP markers. The panel was evaluated for blast resistance in field, under the pressure of the natural blast population, and in growth chamber, using a mixture of three different fungal strains.ResultsThe parallel screening identified 11 accessions showing high levels of resistance in the two conditions, representing potential donors of resistance sources harbored in rice genotypes adapted to temperate conditions. A general higher resistance level was observed in tropical japonica and indica with respect to temperate japonica varieties. The GWAS identified 14 Marker-Traits Associations (MTAs), 8 of which discovered under field conditions and 6 under growth chamber screening. Three MTAs were identified in both conditions; five MTAs were specifically detected under field conditions while three for the growth chamber inoculation. Comparative analysis of physical/genetic positions of the MTAs showed that most of them were positionally-related with cloned or mapped blast resistance genes or with candidate genes whose functions were compatible for conferring pathogen resistance. However, for three MTAs, indicated as BRF10, BRF11-2 and BRGC11-3, no obvious candidate genes or positional relationships with blast resistance QTLs were identified, raising the possibility that they represent new sources of blast resistance.ConclusionsWe identified 14 MTAs for blast resistance using both field and growth chamber screenings. A total of 11 accessions showing high levels of resistance in both conditions were discovered. Combinations of loci conferring blast resistance were identified in rice accessions adapted to temperate conditions, thus allowing the genetic dissection of affordable resistances present in the panel. The obtained information will provide useful bases for both resistance breeding and further characterization of the highlighted resistance loci.
| S-EPMC7544789 | biostudies-literature
Project description:There is unprecedented increase in low-temperature stress (LTS) during post-heading stages in rice as a consequence of the recent climate changes. Quantifying the effect of LTS on yields is key to unraveling the impact of climatic changes on crop production, and therefore developing corresponding mitigation strategies. The present research was conducted to analyze and quantify the effect of post-heading LTS on rice yields as well as yield and grain filling related parameters. A two-year experiment was conducted during rice growing season of 2018 and 2019 using two Japonica cultivars (Huaidao 5 and Nanjing 46) with different low-temperature sensitivities, at four daily minimum/maximum temperature regimes of 21/27 °C (T1), 17/23 °C (T2), 13/19 °C (T3) and 9/15 °C (T4). These temperature treatments were performed for 3 (D1), 6 (D2) or 9 days (D3), at both flowering and grain filling stages. We found LTS for 3 days had no significant effect on grain yield, even when the daily mean temperature was as low as 12 °C. However, LTS of between 6 and 9 days at flowering but not at filling stage significantly reduced grain yield of both cultivars. Comparatively, Huaidao 5 was more cold tolerant than Nanjing 46. LTS at flowering and grain filling stages significantly reduced both maximum and mean grain filling rates. Moreover, LTS prolonged the grain filling duration of both cultivars. Additionally, there was a strong correlation between yield loss and spikelet fertility, spikelet weight at maturity, grain filling duration as well as mean and maximum grain filling rates under post-heading LTS (p < 0.001). Moreover, the effect of post-heading LTS on rice yield can be well quantified by integrating the canopy temperature (CT) based accumulated cold degree days (ACDDCT) with the response surface model. The findings of this research are useful in modeling rice productivity under LTS and for predicting rice productivity under future climates.
| S-EPMC8309334 | biostudies-literature