The yield and quality of rice are directly impacted by floral organ development in rice. Understanding of the floral development mechanism will be useful in genetic improvement of yield and quality. In this study, a rice mutant palea degradation 2 (pd2) in an indica cultivar '8PW33' was obtained after 60Co γ-ray treatment. Analysis of the mutant showed that, compared to the wild type, plant height, total grain number per panicle, and sword leaf width were significantly increased, but the seed setting rate were significantly decreased. The florets of the mutant exhibited degraded palea and sickle-shaped tortuous lemma. Detail examination using scanning electron microscopy revealed that when epidermis of the vane and lemma were normal, epidermis of the palea were arranged tightly, which might result from degraded palea. Genetic analysis supported that this mutation phenotype was controlled by a single recessive gene. Polymorphic analysis of simple sequence repeat markers demonstrated that PD2 gene is located on chromosome 9. With a larger mapping population and more indel markers, we further mapped PD2 gene between 2 indel markers with a physical region of about 82 kb. Within this region, there is a cloned gene REP1 known to control rice palea development. By comparing the DNA sequences of REP1 from pd2 and 8PW33, in combination with the results of phenotypic analysis, we concluded that PD2 is an allele of REP1.
Bacterial leaf streak (BLS) is a devastating rice disease caused by the bacterial pathogen, Xanthomonas oryzae pv. oryzicola (Xoc), which can result in severe damage to rice production worldwide. Based on a total of 510 rice accessions, trialed in two seasons and using six different multi-locus GWAS methods (mrMLM, ISIS EM-BLASSO, pLARmEB, FASTmrMLM, FASTmrEMMA and pKWmEB), 79 quantitative trait nucleotides (QTNs) reflecting 69 QTLs for BLS resistance were identified (LOD > 3). The QTNs were distributed on all chromosomes, with the most distributed on chromosome 11, followed by chromosomes 1 and 5. Each QTN had an additive effect of 0.20 (cm) and explained, on average, 2.44% of the phenotypic variance, varying from 0.00–0.92 (cm) and from 0.00–9.86%, respectively. Twenty-five QTNs were detected by at least two methods. Among them, qnBLS11.17 was detected by as many as five methods. Most of the QTNs showed a significant interaction with their environment, but no QTNs were detected in both seasons. By defining the QTL range for each QTN according to the LD half-decay distance, a total of 848 candidate genes were found for nine top QTNs. Among them, more than 10% were annotated to be related to biotic stress resistance, and five showed a significant response to Xoc infection. Our results could facilitate the in-depth study and marker-assisted improvement of rice resistance to BLS.
SUMMARYFloral organ development influences plant reproduction and crop yield. The mechanism of floral organ specification is generally conserved in angiosperms as demonstrated by the ‘ABC’ model. However, mechanisms underlying the development of floral organs in specific groups of species such as grasses remain unclear. In the genus Oryza (rice), a spikelet consists of a fertile floret sub-tended by a lemma, a palea, two sterile lemmas and rudimentary glumes. To understand how the lemma is formed, a curve-shaped lemma-distortion1 (ld1) mutant was identified. Genetic analysis confirmed that the ld1 mutant phenotype was due to a single recessive gene mutation. Using a large F2 population, the LD1 gene was mapped between markers Indel-7-15 and Indel-7-18, which encompassed a region of 15·6 kilo base pairs (kbp). According to rice genome annotations, two putative genes, LOC_Os07g32510 and LOC_Os07g32520, were located in this candidate region. However, DNA sequencing results indicated only 1 base pair (bp) substitution (T⇨C) was found in LOC_Os07g32510 between the wild-type and the ld1 mutant. Thus LOC_Os07g32510, encoding a DNA binding with one zinc finger (DoF) containing protein, was the candidate gene for LD1. Further analysis showed that mutation of the amino acid cysteine (C) to arginine (R) was likely to lead to zinc finger protein deactivation. Phylogenetic and conservation analysis of the gene from different species revealed that cysteine was critical to LD1 function. As a new gene controlling lemma development, the study of LD1 could provide insights into rice floral organ formation mechanisms.
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