Euphytica

Adorada, Dante; Stodart, B.; Cruz, C.; Gregorio, G.; Pangga, I.; Ash, G.

doi: 10.1007/s10681-012-0804-zpmid: N/A

Sheath lesions, grain sterility and grain discolouration of rice caused by Pseudomonas fuscovaginae can cause yield losses of up to 100 %. The most sustainable method of managing this disease is the use of host plant resistance. To identify sources of resistance an inoculation method that is practical, rapid and reliable is needed. We compare three different inoculation methods. Results showed that the pin-prick method is appropriate for identifying sources of resistance to P. fuscovaginae, while the spray method could be useful for mass screening of rice genotypes. The seed-soaking method was also evaluated and has showed potential in detection of early disease resistance. A total of 16 Multiparent Advanced Generation Inter-Crosses and 20 OryzaSNP set varieties from the International Rice Research Institute were evaluated using the pin-prick and seed-soaking methods. All growth stages were susceptible to the pathogen and the 107 cfu mL−1 inoculum concentration was optimal for discriminating between resistant and susceptible genotypes. For the pin-prick method, a single point assessment of disease severity at 14 days post-inoculation could be used instead of the AUDPC values to classify genotypes. An index of reduction in seedling height 10 days after seed soaking was established for the classification of the genotypes reaction to the disease. Resistant varieties identified using both the pin-prick and seed-soaking methods could be verified for use in disease resistance breeding programs. Of the 36 genotypes evaluated 22 were found to be resistant at the late booting or early panicle exsertion stage by pin-prick method, while 25 were resistant at the seed to germination stage. No correlation was found between the resistance classification of varieties between the two inoculation methods, indicating that there could be different mechanisms of resistance to P. fuscovaginae in rice.

Yasuda, Kanako; Tsukiyama, Takuji; Karki, Shanta; Okumoto, Yutaka; Teraishi, Masayoshi; Saito, Hiroki; Tanisaka, Takatoshi

doi: 10.1007/s10681-012-0810-1pmid: N/A

Miniature Ping (mPing) is the first active miniature inverted-repeat transposable element to be identified in rice, and its mobilization is activated by stress treatments. We have examined the mobilization of mPing in four NERICA (New Rice for Africa) lines and 13 interspecific lines. All 17 lines are inbred progenies derived from crosses between Oryza sativa variety WAB56-104 as the recurrent parent and the O. glaberrima variety CG14 as the donor parent. We found that 16 of the 17 lines studied inherited mPing together with its autonomous partner, Pong, from WAB56-104. Transposon display of mPing disclosed polymorphic banding patterns among these lines. Most importantly, seven of the lines displayed clear polymorphic banding patterns for mPing, indicating that mPing might have been mobilized in these lines. Locus-specific PCR analysis also confirmed the mobilization of mPing. These results signify that interspecific hybridization may activate the transposition of mPing. Based on these results, we discuss the potential use of the mPing system as an efficient tool for gene tagging in interspecific hybrid rice.

Lu, Bingyue; Yang, Chunyan; Xie, Kun; Zhang, Long; Wu, Tao; Li, Linfang; Liu, Xi; Jiang, Ling; Wan, Jianmin

doi: 10.1007/s10681-012-0822-xpmid: N/A

Improving grain-quality is an important goal in rice breeding programs. One vital step is to find major quantitative trait loci (QTLs) for quality related traits and then investigate the relationships among them. We crossed ‘N22’, an indica variety with good appearance but low grain weight, to a japonica variety, ‘Nanjing35’, with superior grain yield but poor appearance. This enabled us to construct an F2 population and a set of backcross inbred lines (BILs) for QTL-mapping for the traits related grain appearance. In all, 37 QTLs were identified for grain length (GL), grain width (GW), grain thickness (GT), thousand-grain weight (TGW), and the percentage of grains with chalkiness (PGWC). Of these, 17 QTLs detected from 184 plants in the F2 population explained 4.97–27.26 % of the phenotypic variance, another 20 QTLs were identified using BILs from 2009 to 2010. Quantitative trait loci for major effects were detected in different populations and across years. A new QTL hot spot (marker interval RM504–RM520) was found on Chromosome 3, which harbored QTLs for GL, GW, GT, and TGW. Among our five examined traits, grain shape was significantly correlated with TGW and PGWC. The PGWC values of two heavier grains BILs, L93, and L145 are much lower than Nanjiing35, the analysis of genotype showed that this greater weight may due to the locus for GL occurring within RM504–RM520 on Chromosome 3. Therefore, those two lines will allow us to develop a long-grain high-yield rice variety with less chalkiness.

Luo, Zhixiang; Piao, Zhongze; Zhou, Xiaojing; Yang, Tianfu; Yang, Runqing

doi: 10.1007/s10681-012-0825-7pmid: N/A

Usually, statistical methods for mapping quantitative trait loci (QTL) require that the phenotypes follow the normal distribution and therefore may not be appropriate to analyze survival traits of skewed distribution. As a result, parametric and semi-parametric models in survival analysis are incorporated into the framework of the interval mapping for survival trait loci. Through formulating the effects of the QTL genotype on the survival time with a Cox proportional hazards model, we construct a general parametric model for mapping survival trait loci, in which baseline hazard function is selectable for goodness of fit to the effects of QTL genotype on survival curve. Bayesian information criterion is used to choose the optimal baseline hazard function with maximum likelihood and parsimonious parameters. Heading time, defined by days from sowing to heading is a typical survival trait. In this study, we apply the mapping method to locate QTL for heading time in rice and conclude that among the six commonly used survival distributions, Gamma distribution is the optimal baseline hazard function and by which, four QTLs are identified.

Sun, Pingyong; Liu, Jinling; Wang, Yue; Jiang, Nan; Wang, Suhua; Dai, Yangshuo; Gao, Jia; Li, Zhiqiang; Pan, Sujun; Wang, Dan; Li, Wei; Liu, Xionglun; Xiao, Yinghui; Liu, Erming; Wang, Guo-Liang; Dai, Liangying

Dixit, N.; Dokku, P.; Amitha Mithra, S.; Parida, S.; Singh, A.; Singh, N.; Mohapatra, T.

doi: 10.1007/s10681-012-0852-4pmid: N/A

GW2, a grain weight quantitative trait locus (QTL) in rice encodes a ring type E-3 ubiquitin ligase. A single nucleotide deletion at the 346th nucleotide position in the ligase domain of GW2 was earlier reported to result in higher grain weight in rice. The present study aimed at validating the known functional polymorphism and identifying additional natural genetic variation if any, in the region that included the functional domain of GW2 in a set of indica and aromatic genotypes for which ninety three rice genotypes were phenotyped for grain length, grain width and 100 grain weight. A wide range of variation was observed for these traits. PCR amplification and sequencing of GW2 target region revealed absence of insertion/deletion (InDel) at the 346th position which suggested that the genetic variation in grain weight in Basmati and non-Basmati indica genotypes was not explained by this InDel. However, four new single nucleotide polymorphisms (SNPs) were discovered at nucleotide positions 406, 461, 466 and 501 in the fifth exon and one InDel each in second and fourth introns. Only two of these SNPs, at positions 461 and 501 led to amino acid substitutions. A total of 10 haplotypes were constructed based on these four SNPs which could be regrouped into four categories based on their amino acid substitutions. Association genetic analysis of these haplotypes with different grain traits revealed a moderate association with grain width (R2 = 0.18 at P < 0.05). Thirteen haplotypes constructed using both intronic and exonic polymorphisms did not have any association with grain traits.

Manangkil, O.; Vu, H.; Mori, N.; Yoshida, S.; Nakamura, C.

doi: 10.1007/s10681-012-0857-zpmid: N/A

Submergence-induced suppression of seedling vigor is a serious constraint particularly in the direct seeding rice cultivation system. To identify quantitative trait loci (QTLs) associated with seedling vigor in rice under submergence, a mapping population of 98 Backcross Inbred Lines derived from a cross of Nipponbare/Kasalath//Nipponbare was used. Phenotypic evaluation of seedling vigor under submergence was based on shoot length (SHL), root length (RTL) and shoot fresh weight (SFW) using a test tube bioassay method. Thirty-two putative QTLs were detected among which 7 were for SHL, 11 for RTL and 14 for SFW. Phenotypic evaluation was also made of the parental lines and a set of 54 chromosome segment substitution lines in which Nipponbare segments were substituted for by their homologous Kasalath segments covering the entire rice genome. Two QTLs with more than 10 % contribution to the total phenotypic variance were verified for SHL, and at least one for RTL and six for SFW on chromosomes 1, 3, 4, 6 and 7 at the 1 % significance level. Among these, all but two showed reductions in one, two or all three traits. Our present and previous results suggest that the Nipponbare genome has a potential to improve seedling vigor under submergence and that japonica germplasms can be used to breed for this important trait in indica rice.