Bulked segregant analysis to detect main effect QTL associated with grain quality parameters in Basmati 370/ASD 16 cross in rice Oryza sativa L) using SSR markers

Abstract

In the present study a population consisting of 247 F 2 individuals from the cross between Basmati 370, a superior quality basmati variety and ASD16, a non-basmati high-yielding variety was analyzed for their segregation pattern of grain length (GL), grain breadth (GB), cooked grain length (CGL), cooked grain breadth (CGB), and gelatinization temperature (GT). Except GT, all other traits showed normal distribution indicating the polygenic control over the traits. The correlation analysis between traits indicated that GT had positive significant association with GL (0.125), and CGL (0.243). To identify main effect QTL (MQTL) for the above grain quality traits, both the parents were surveyed with 86 primer pairs of simple sequence repeats (SSR). The parental survey revealed 63.95% polymorphism between parents. In order to detect the MQTL associated with grain quality traits, a strategy of combining the DNA pooling from selected segregants and genotyping was adopted. The number of individuals forming the bulk influenced the identification of putative marker(s) for each of the traits. The association of putative markers identified based on DNA pooling from selected segregants was established by Single Marker Analysis (SMA). The results of SMA revealed that SSR markers, RM225 on chromosome #6 and RM247 on chromosome #12 showed significant association with GB and CGB respectively. It is established that molecular marker analysis involving DNA pooling of phenotypic extremes and selective genotyping helps to detect MQTL for complex traits involving early segregating generations. The molecular marker analysis involving the DNA pooling of phenotypic extremes could be a useful strategy to detect the genetic loci with major effects of other complex grain quality traits in rice.

Analysing genetic control of cooked grain traits and gelatinization temperature in a double haploid population of rice by quantitative trait loci mapping

“…Yano and Sasaki (1997) suggested that rice grain quality is under the inXuence of quantitative alleles showing continuous variation. Earlier genetic investigations reported monogenic (Chao 1928;Ramaiah et al 1931), digenic (Bollich 1957) and trigenic (Ramiah and Parthasarathy 1933) inheritance for grain length besides polygenic inheritance for grain length and breadth (Jones et al 1935;Chang 1974), but the results are inconclusive and limited (Govindaraj et al 2005). Cooking quality of rice can be attributed to three major grain properties viz., grain elongation, volume expansion and water absorption (Ge et al 2005).…”

“…Earlier genetic investigations reported monogenic (Chao 1928;Ramaiah et al 1931), digenic (Bollich 1957) and trigenic (Ramiah and Parthasarathy 1933) inheritance for grain length besides polygenic inheritance for grain length and breadth (Jones et al 1935;Chang 1974), but the results are inconclusive and limited (Govindaraj et al 2005). Cooking quality of rice can be attributed to three major grain properties viz., grain elongation, volume expansion and water absorption (Ge et al 2005). It is determined by the physicochemical properties of the endosperm viz., amylose content (AC) (Webb 1980;Juliano 1985), gel consistency (GC) (Cagampang et al 1973) and gelatinization temperature (GT) (Little et al 1958).…”

“…Good cooking quality was associated with greater linear elongation, less volume expansion and less water absorption (Tang 1987). The raw grain dimensions like grain length and breadth, changes occurring to these traits on cooking and the temperature at which rice grain becomes gelatinous during cooking (GT) are measured for determining overall cooking quality (Govindaraj et al 2005). GT is often indirectly estimated through alkali spreading value (ASV).…”

Bulked segregant analysis for relative water content to detect quantitative trait loci in wheat under drought stress

“…Typically, for GWM182, 5 of 10 individuals possessed tolerant bulk profiles (Figure 2). Some studies have reported using BSA to find links for specific genes (Michelmore et al, 1991;Govindaraj et al, 2005). One-way ANOVA was carried out using marker genotypes as groups.…”

Detection of a single nucleotide polymorphism (SNP) DNA marker linked to cocoon traits in the mulberry silkworm, Bombyx mori (Lepidoptera: Bombycidae)

“…This technique was successfully used to identify DNA markers linked to the downy mildew resistance gene in lettuce (Michelmore et al, 1991), leaf rust resistance in barley (Poulsen et al, 1995), malaria and nematode resistance genes in mosquitoes (Severson et al, 1999), powdery mildew resistance gene in wheat (Chantret et al, 2000), sex determination in aphids (Gadau et al, 2001), vaccine response in chicks (Kaiser et al, 2002), QTL for grain quality in rice (Govindaraj et al, 2005), sex expression in shrimps (Khamnamtong et al, 2006), genetic mapping in zebra fish (Bradley et al, 2007), clubroot resistance genes in oilseed rape (Werner et al, 2008), red wing patterning in Heliconius butterflies (Baxter et al, 2008), isolation of sex-linked SCAR markers in yellow catfish (Wang et al, 2009), and powdery mildew resistance gene in soybean (Kang & Mian, 2010).…”