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28 May 2018, Volume 25 Issue 3 Previous Issue    Next Issue
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QTL-Seq Identified a Major QTL for Grain Length and Weight in Rice Using Near Isogenic F2 Population Yaobin Qin, Peng Cheng, Yichen Cheng, Yue Feng, Derun Huang, Tingxu Huang, Xianjun Song, Jiezheng Ying 2018, 25(3): 121-131.  DOI: 10.1016/j.rsci.2018.04.001 Abstract ( )   HTML ( )   PDF (988KB) ( )   Mapping and isolation of quantitative trait loci (QTLs) or genes controlling grain size or weight is very important to uncover the molecular mechanisms of seed development and crop breeding. To identify the QTLs controlling grain size and weight, we developed a near isogenic line F2 (NIL-F2) population, which was derived from a residual heterozygous plant in an F7 generation of recombinant inbred line (RIL). With the completion of more than 30× whole genome re-sequencing of the parents, two DNA bulks for large and small grains, a total of 58.94 Gb clean nucleotide data were generated. A total of 455 262 single nucleotide polymorphisms (SNPs) between the parents were identified to perform bulked QTL-seq. A candidate genomic region containing SNPs strongly associated with grain length and weight was identified from 15 to 20 Mb on chromosome 5. We designated the major QTL in the candidate region as qTGW5.3. Then, qTGW5.3 was further validated with PCR-based conventional QTL mapping method through developing simple sequence repeat and Insertion/Deletion markers in the F2 population. Furthermore, recombinants and the progeny tests delimited the candidate region of qTGW5.3 to 1.13 Mb, flanked by HX5009 (15.15 Mb) and HX5003 (16.28 Mb). A set of NILs, selected from the F2 population, was developed to evaluate the genetic effect of qTGW5.3. Significant QTL effects were detected on grain length, grain width and 1000-grain weight of H12-29 allele with 1.14 mm, -0.11 mm and 3.11 g, which explained 99.64%, 95.51% and 97.32% of the phenotypic variations, respectively.

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A Novel and Pleiotropic Factor SLENDER GRAIN3 Is Involved in Regulating Grain Size in Rice Zhongkang Wang, Dongdong Zeng, Ran Qin, Jialin Liu, Chunhai Shi, Xiaoli Jin 2018, 25(3): 132-141.  DOI: 10.1016/j.rsci.2018.02.004 Abstract ( )   HTML ( )   PDF (984KB) ( )   Grain size is frequently selected during domestication and breeding. It influences the preferences of consumers, thus affecting the commercial value of rice. In present study, a mutant named as SLENDER GRAIN3 (sg3) was identified from cultivar Zhenong 41 (Oryza sativa L. ssp. indica) with ethyl methanesulfonate (EMS) treatment. Histological analysis showed that the slender grain of sg3 mutant resulted from increased cell division longitudinally and decreased cell division horizontally. Compared with the wild type Zhenong 41, starch granules in sg3 mutant were more closely packed, thus decreasing the chalkiness. Moreover, grain yield per plant in sg3 mutant was improved by 14%. By map-based cloning, SG3 was located on the long arm of chromosome 3 with a physical distance of 82 kb, and a 9-bp deletion in the 5′-UTR of LOC_Os03g27110 was identified, which upregulated the expression level significantly. Moreover, a molecular marker for SG3 was developed to identify the grain size during the early generation breeding in rice. The novel factor SG3 regulated the grain size mainly through changing the cell division and the endosperm formation in rice.

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Responses of Four Rice Varieties to Elevated CO2 and Different Salinity Levels Kazemi Sheidollah, Reza Eshghizadeh Hamid, Zahedi Morteza 2018, 25(3): 142-151.  DOI: 10.1016/j.rsci.2018.04.002 Abstract ( )   HTML ( )   PDF (691KB) ( )   This study was carried out in 2014 at Isfahan University of Technology, Iran, to evaluate the responses of four rice varieties (Neda, Deylamani, Shiroudi and Domsorkh) to ambient (360 ± 50 µmol/mol) and elevated (700 ± 50 µmol/mol) air carbon dioxide (CO2) concentrations under four salinity levels (0, 30, 60 and 90 mmol/L NaCl). There was significant variation among rice varieties in response to elevated CO2 concentration under the four salinity levels. Under non-saline condition, elevated CO2 increased the dry weight of Neda, Deylamani and Domsorkh by 8%, 50% and 8%, respectively, but reversely decreased that of Shiroudi by 34%. Increasing CO2 concentration significantly reduced the negative effects of salinity on Shiroudi, but these effects were even increased in Deylamani and Domsorkh under all the salinity levels and in Neda only under 30 and 60 mmol/L NaCl. Significant correlations were established between plant dry weight, SPAD value and leaf area under both CO2 levels. However, this trend was observed only at ambient CO2 concentration in the presence of soluble carbohydrates. The results revealed the genotype and salinity dependence of the effects of CO2 concentrations on the rice traits investigated.

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Levels of Crotonaldehyde and 4-hydroxy-(E)-2-nonenal and Expression of Genes Encoding Carbonyl-Scavenging Enzyme at Critical Node During Rice Seed Aging Shenzao Fu, Guangkun Yin, Xia Xin, Shuhua Wu, Xinghua Wei, Xinxiong Lu 2018, 25(3): 152-1604.  DOI: 10.1016/j.rsci.2018.04.003 Abstract ( )   HTML ( )   PDF (639KB) ( )   The critical node (CN) is an important stage during seed aging, which is related to effective genebank conservation. Previous studies have demonstrated that proteins undergo carbonylated modification at the CN in rice, indicating oxidative damage. However, the levels of reactive carbonyl species (RCS) and the associated scavenging system at the CN are largely unknown. In this study, we optimized methods for the extraction and analysis of RCS from dry rice embryos. In order to acquire seeds at the CN, rice seeds were subjected to natural conditions for 7, 9, 11 and 13 months, and the seed germination rates were reduced to 90%, 82%, 71% and 57%, respectively. We chose the stage with seed germination rate of 82% as the CN according to the rice seed vigor loss curve. The levels of crotonaldehyde and 4-hydroxy-(E)-2-nonenal (HNE) were significantly increased at the CN. In addition, genes encoding carbonyl-scavenging enzyme, including OsALDHs and OsAKRs, were significantly down-regulated at the CN, and reductions in the expression of OsALDH2-2, OsALDH2-5, OsALDH3-4, OsALDH7, OsAKR1 and OsAKR2 in particular could be responsible for RCS accumulation. Thus, the accumulations of crotonaldehyde and HNE and down-regulation of genes encoding carbonyl-scavenging enzyme might be related to an accelerating loss of seed viability at the CN.

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Mapping of Hd-6-2 for Heading Date Using Two Secondary Segregation Populations in Rice Hua Zhang, Xu Liu, Yongyi Yang, Ning Xuan, Fangyin Yao 2018, 25(3): 161-168.  DOI: 10.1016/j.rsci.2018.02.005 Abstract ( )   HTML ( )   PDF (596KB) ( )   Heading date is one of the most important traits for rice adaption to different cultivation areas and crop seasons. In this study, two single segment substitution lines (SSSLs), W31-41-61-3-11-3-6-7 (W31-SSSL) and W32-59-80-2-11-1-10 (W32-SSSL) with substituted intervals derived from the donor parents IR66897B (W31) and IR66167-27-5-1-6 (W32), respectively, with Huajingxian 74 (HTX74) were found to comprise a gene for extremely late-heading date, and the gene was tentatively designated as Hd-6-2. Two secondary F2 segregating populations were developed by crossing the two heterozygous SSSLs with HJX74 to map Hd-6-2 gene. According to phenotype analysis of the two mapping populations, the late heading date trait was controlled by a major recessive gene. In the segregation population derived from W31-SSSL, Hd-6-2 was mapped on chromosome 6 between PSM677 and RM204 with the genetic distances of 1.3 and 2.7 cM, respectively. In the population of W32-SSSL, the gene for heading date was mapped to the similar region as Hd-6-2 and co-segregated with PSM672. The sequence alignment of Hd3a in the coding domains and promoter regions of HJX74 and W31-SSSL are completely consistent, whereas there was a great difference between W32-SSSL and HJX74, suggesting that Hd3a could hardly be the main cause of the heading date variation in W31-SSSL, but it was probably the main reason for the change of heading stage in W32-SSSL.

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Natural Colonization of Rice by Arbuscular Mycorrhizal Fungi in Different Production Areas Bernaola Lina, Cange Grace, O. Way Michael, Gore Jeffrey, Hardke Jarrod, Stout Michael 2018, 25(3): 169-174.  DOI: 10.1016/j.rsci.2018.02.006 Abstract ( )   HTML ( )   PDF (421KB) ( )   Interactions between plants and soil microorganisms can influence the other interactions in which plants participate, including interactions with herbivores. Many fungi, including arbuscular mycorrhizal fungi (AMF), form symbiotic relationships with the roots they inhabit, and potentially alter defense against pests. The objective of this study was to document the extent of root colonization by AMF on non-flooded rice plants grown under conditions typical of commercial fields. We hypothesized that AMF naturally colonized rice plants in different rice producing field locations. Rice plant samples were collected from areas across the southern United States, including Texas, Mississippi, Arkansas and two research stations in Louisiana. We quantified the amount of AMF colonization in insecticide-free rice plants over three consecutive years (2014-2016). The results revealed natural colonization of AMF in all rice producing areas. In all the three years of survey, rice-AMF associations were the greatest in Arkansas followed by Mississippi and Texas. This research will help draw attention to natural colonization of AMF in rice producing areas that can impact future rice research and production by facilitating agricultural exploitation of the symbiosis.