Detection of quantitative trait locus for leaffolder (Cnaphalocrocis medinalis (Guenée)) resistance in rice on linkage group 1 based on damage score and flag leaf width

Abstract

Rice leaffolder (RLF) (Cnaphalocrocis medinalis (Guené e) is a destructive and widespread insect pest throughout the rice growing regions in Asia. The genetics of resistance to RLF in rice is very complex and not thoroughly explored. The present study was conducted to detect the quantitative trait loci (QTL) associated with RLF resistance involving 176 recombinant inbred lines (RILs) of F 8 generation derived from a cross between IR36, a leaffolder susceptible variety and TNAULFR831311, a moderately resistant indica rice culture. Simple sequence repeat (SSR) markers were used to construct specific linkage groups of rice. All the RILs were screened to assess their level of resistance to RLF by measuring the leaf area damaged. Besides this, the length and width of the flag leaf of each RIL were measured since these two parameters were considered as correlated traits to the RLF resistance in rice. All the above parameters observed across the RILs showed quantitative variation.Correlation analysis revealed that damage score based on greenhouse screening was positively correlated with length and width of the flag leaf. Out of 364 SSR markers analysed, 90 were polymorphic between the parents. Multi-point analysis carried out on segregating 69 SSR marker loci linkage group wise resulted in construction of linkage map with eleven groups of 42 SSR markers. Through single marker analysis, 19 SSR markers were found to have putative association with the three phenotypic traits studied. Of these markers, RM472 was identified as a locus having major effect on RLF resistance trait based on length of the flag leaf. Interval mapping detected two QTLs on linkage group 1. Among these QTLs, the QTL flanked by RM576-RM3412 were found to be associated with width of the flag leaf and RLF resistance. The putative SSR markers associated with leaffolder resistance identified in the present study may be one of the loci contributing resistance to RLF in rice.

Identification of QTLs for high grain yield and component traits in New Plant Types of rice

“…However, Marathi et al (2012) reported that RM5709 marker was linked with qSPP-4.1 , indicating the pleiotropic effect of qPL4.1 on panicle length. The present study reported that a total of 14 SSRs were associated with FLW out of them 3 SSRs RM297, RM5709, RM1132) were reported previously [28,29,31,67,68]. Four SSRs, RM447, RM297, RM5709 and RM285 have been identified for flag leaf length (FLL) in QTL regions of qFLL8.1 , qFLL-1.1 [29], qFLL-4.1a and qFLL9.1 , respectively.…”

“…The present study reported that a total of 14 SSRs were associated with FLW out of them 3 SSRs RM297, RM5709, RM1132) were reported previously [28,29,31,67,68]. Four SSRs, RM447, RM297, RM5709 and RM285 have been identified for flag leaf length (FLL) in QTL regions of qFLL8.1 , qFLL-1.1 [29], qFLL-4.1a and qFLL9.1 , respectively. Out of the above, two markers, RM297 and RM5709 were also associated with QTLs for flag leaf width(FLW), qFLW-1.1 and qFLW4.1 , respectivelly due to pleiotropic effects [28, 29].…”

“…Twenty SSRs were having association with more than one traits and have been reported in the gramene-database (http://www.gramene.org/) by earlier studies (Table 6) [28,29,49,89]. These were significantly associated with yield controlling complex traits viz., PH, DFF, SLBR, TL, PL, FLL, FLW, FG, TG, TGW and YLD and supposed to have played a significant role in yield enhancement (Table 5, Table 6, Fig 8).…”

“…Four SSRs, RM447, RM297, RM5709 and RM285 have been identified for flag leaf length (FLL) in QTL regions of qFLL8.1 , qFLL-1.1 [29], qFLL-4.1a and qFLL9.1 , respectively. Out of the above, two markers, RM297 and RM5709 were also associated with QTLs for flag leaf width(FLW), qFLW-1.1 and qFLW4.1 , respectivelly due to pleiotropic effects [28, 29]. Similar reports corroborate the present finding of marker-trait association for RM1132 apart from three other reported markers [31].…”

Development and characterization of microsatellite markers in the fungus Antrodia cinnamomea from dbEST database

“…Recently, internal transcribed spacer (ITS) markers were developed to identify and distinguish the different Antrodia species (Chiu 2007). However, microsatellites or simple sequence repeats (SSRs) were commonly used for diversity analysis, quantitative trait loci (QTL) mapping and population genetic studies of many organisms (Thomson et al 2007;Selvaraju et al 2007;Zhang et al 2008) because of their abundance, multiallelic nature, co-dominance, easily detectable nature and reproducibility. As the development of genomic SSR markers are expensive, resource intensive and time consuming, highly transferable expressed sequence tag (EST)-derived SSR markers can be used to evaluate the genetic variation of transcribed genes in A. cinnamomea.…”