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[学术文献 ] Genetic behavior of earliness and yield traits of some rice (Oryza sativa L.) genotypes 进入全文
SAUDI JOURNAL OF BIOLOGICAL SCIENCES
Rice (Oryza sativa L.) is a critical staple food crop that provides more than half of the world's population with its primary nutritional source. Breeders and growers of rice would profit from robust genotypes with improved morphological and yield-related characteristics. The aim of this work is to determine the nature and magnitude of gene action on yield quantity and quality, to define the best combinations of earliness and yield characters, develop hybrids that perform better on yield quantity and quality. Three replications were used in the experiment's randomized complete block design (RCBD). During the 2016 season, seven different parents, namely Sakha 101, Sakha 104, Sakha 105, Giza 177, Black rice 1, Black rice 2, and Black rice 3, were crossed using A 7 x 7 half-diallel set analysis without reciprocals to generate 21 F1 crosses. The results indicated that genotype-dependent mean squares were very significant for main characteristics. Significant combining ability SCA variance estimates were more considerable than general combining ability (GCA) variance for all characters except days to 50% flowering. It demonstrated that both additive and non-additive genetic variance played a role in expressing the attributes investigated. The Parents, Black rice, Sakha 105, and Sakha 101, were recognized as the best general combiner for most growth and yield attributes. Sakha105 x Black Rice 1, Sakha105 x Black Rice 2, Sakha101 x Sakha104, Sakha105 x Giza 177, and Sakha101 x Giza 177 all demonstrated non-additive gene activity for the majority of maturity and yield traits. Heterosis breeding would be most efficient for qualities where high performance was determined by dominance and dominance gene effects. The increased yield of crosses results from parents with a diverse genetic background and genetic diversity.(c) 2022 The Authors. Published by Elsevier B.V. on behalf of King Saud University. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).
[学术文献 ] Intelligent Identification and Features Attribution of Saline-Alkali-Tolerant Rice Varieties Based on Raman Spectroscopy 进入全文
Web of Science
Planting rice in saline-alkali land can effectively improve saline-alkali soil and increase grain yield, but traditional identification methods for saline-alkali-tolerant rice varieties require tedious and time-consuming field investigations based on growth indicators by rice breeders. In this study, the Python machine deep learning method was used to analyze the Raman molecular spectroscopy of rice and assist in feature attribution, in order to study a fast and efficient identification method of saline-alkali-tolerant rice varieties. A total of 156 Raman spectra of four rice varieties (two saline-alkali-tolerant rice varieties and two saline-alkali-sensitive rice varieties) were analyzed, and the wave crests were extracted by an improved signal filtering difference method and the feature information of the wave crest was automatically extracted by scipy.signal.find peaks. Select K Best (SKB), Recursive Feature Elimination (RFE) and Select F Model (SFM) were used to select useful molecular features. Based on these feature selection methods, a Logistic Regression Model (LRM) and Random Forests Model (RFM) were established for discriminant analysis. The experimental results showed that the RFM identification model based on the RFE method reached a higher recognition rate of 89.36%. According to the identification results of RFM and the identification of feature attribution materials, amylum was the most significant substance in the identification of saline-alkali-tolerant rice varieties. Therefore, an intelligent method for the identification of saline-alkali-tolerant rice varieties based on Raman molecular spectroscopy is proposed.
[学术文献 ] Balancing selection and wild gene pool contribute to resistance in global rice germplasm against planthopper 进入全文
JOURNAL OF INTEGRATIVE PLANT BIOLOGY
Interactions and co-evolution between plants and herbivorous insects are critically important in agriculture. Brown planthopper (BPH) is the most severe insect of rice, and the biotypes adapt to feed on different rice genotypes. Here, we present genomics analyses on 1,520 global rice germplasms for resistance to three BPH biotypes. Genome-wide association studies identified 3,502 single nucleotide polymorphisms (SNPs) and 59 loci associated with BPH resistance in rice. We cloned a previously unidentified gene Bph37 that confers resistance to BPH. The associated loci showed high nucleotide diversity. Genome-wide scans for trans-species polymorphisms revealed ancient balancing selection at the loci. The secondarily evolved insect biotypes II and III exhibited significantly higher virulence and overcame more rice varieties than the primary biotype I. In response, more SNPs and loci evolved in rice for resistance to biotypes II and III. Notably, three exceptional large regions with high SNP density and resistance-associated loci on chromosomes 4 and 6 appear distinct between the resistant and susceptible rice varieties. Surprisingly, these regions in resistant rice might have been retained from wild species Oryza nivara. Our findings expand the understanding of long-term interactions between rice and BPH and provide resistance genes and germplasm resources for breeding durable BPH-resistant rice varieties.
[学术文献 ] Genotypic Variation in Nutrient Uptake Requirements of Rice Using the QUEFTS Model 进入全文
AGRONOMY-BASEL
Nutrient requirements for single-season rice using the quantitative evaluation of the fertility of tropical soils (QUEFTS) model in China have been estimated in a previous study, which involved all the rice varieties; however, it is unclear whether a similar result can be obtained for different rice varieties. In this study, data were collected from field experiments conducted from 2016 to 2019 in Zhejiang Province, China. The dataset was separated into two parts: japonica/indica hybrid rice and japonica rice. To produce 1000 kg of grain, 13.5 kg N, 3.6 kg P, and 20.4 kg K were required in the above-ground plant dry matter for japonica/indica hybrid rice, and the corresponding internal efficiencies (IEs) were 74.0 kg grain per kg N, 279.1 kg grain per kg P, and 49.1 kg grain per kg K. For japonica rice, 17.6 kg N, 4.1 kg P, and 23.0 kg K were required to produce 1000 kg of grain, and the corresponding IEs were 56.8 kg grain per kg N, 244.6 kg grain per kg P, and 43.5 kg grain per kg K. Field validation experiments indicated that the QUEFTS model could be used to estimate nutrient uptake of different rice varieties. We suggest that variety should be taken into consideration when estimating nutrient uptake for rice using the QUEFTS model, which would improve this model.
[学术文献 ] Whole-Genome Sequencing of 117 Chromosome Segment Substitution Lines for Genetic Analyses of Complex Traits in Rice 进入全文
RICE
Rice is one of the most important food crops in Asia. Genetic analyses of complex traits and molecular breeding studies in rice greatly rely on the construction of various genetic populations. Chromosome segment substitution lines (CSSLs) serve as a powerful genetic population for quantitative trait locus (QTL) mapping in rice. Moreover, CSSLs containing target genomic regions can be used as improved varieties in rice breeding. In this study, we developed a set of CSSLs consisting of 117 lines derived from the recipient 'Huanghuazhan' (HHZ) and the donor 'Basmati Surkb 89-15' (BAS). The 117 lines were extensively genotyped by whole-genome resequencing, and a high-density genotype map was constructed for the CSSL population. The 117 CSSLs covered 99.78% of the BAS genome. Each line contained a single segment, and the average segment length was 6.02 Mb. Using the CSSL population, we investigated three agronomic traits in Shanghai and Hangzhou, China, and a total of 25 QTLs were detected in both environments. Among those QTLs, we found that RFT1 was the causal gene for heading date variance between HHZ and BAS. RFT1 from BAS was found to contain a loss-of-function allele based on yeast two-hybrid assay, and its causal variation was a P to S change in the 94th amino acid of the RFT1 protein. The combination of high-throughput genotyping and marker-assisted selection (MAS) is a highly efficient way to construct CSSLs in rice, and extensively genotyped CSSLs will be a powerful tool for the genetic mapping of agronomic traits and molecular breeding for target QTLs/genes.
[学术文献 ] Rice Brittle Culm19 Encoding Cellulose Synthase Subunit CESA4 Causes Dominant Brittle Phenotype But has No Distinct Influence on Growth and Grain Yield 进入全文
RICE
Background Mechanical strength is a crucial agronomic trait in rice (Oryza sativa), and brittle mutants are thought suitable materials to investigate the mechanism of cell wall formation. So far, almost all brittle mutants are recessive, and most of them are defected in multiple morphologies and/or grain yield, limiting their application in hybrid breeding and in rice straw recycling. Results We identified a semi-dominant brittle mutant Brittle culm19 (Bc19) isolated from the japonica variety Nipponbare through chemical mutagenesis. The mutant showed the same apparent morphologies and grain yield to the wild type plant except for its weak mechanical strength. Its development of secondary cell wall in sclerenchyma cells was affected, along with reduced contents of cellulose, hemicellulose, lignin and sugars in culms and leaves. Positional cloning suggested that the Bc19 gene was allelic to OsCESA4, encoding one of the cellulose synthase A (CESA) catalytic subunits. In this mutant, a C-to-T substitution occurred in the coding sequence of BC19, causing the P507S missense mutation in its encoded product, which was located in the second cytoplasmic region of the OsCESA4 protein. Furthermore, introducing mutant gene Bc19 into the wild-type plant resulted in brittle plants, confirming that the P507S point mutation in OsCESA4 protein was responsible for the semi-dominant brittle phenotype of Bc19 mutant. Reverse correlation was revealed between cellulose contents and expression levels of mutant gene Bc19 among the homozygous mutant, the hybrid F-1 plant, and the Bc19 overexpression transgenic plants, implying that gene Bc19 might affect cellulose synthesis in a dosage-dependent manner. Conclusions Bc19, a semi-dominant brittle mutant allele of gene OsCESA4, was identified using map-based cloning approach. The mutated protein of Bc19 possessing the P507S missense mutation behaved in a dosage-dependent semi-dominant manner. Unique brittle effect on phenotype and semi-dominant genetic quality of gene Bc19 indicated its potential application in grain-straw dual-purpose hybrid rice breeding.
