V. S. Rao

Identification of inter simple sequence repeat (ISSR) markers associated with seed size in wheat

Abstract The feasibility of identifying inter-simple sequence repeat markers associated with seed weight in hexaploid wheat was tested using 113 recombinant inbred lines developed by the single-seed descent method, from a cross between Rye selection111, an Indian genetic stock obtained through the introgression of genes for bold seed size from rye, and Chinese Spring having small seed size. Three markers were associated with low seed size with gene effects of 14.8%, 9.5%, and 6%, while four markers with contributions of 8%, 4.66%, 2.92% and 2.61% were found to be linked to high seed size, together contributing 31% of the phenotypic variance in seed size. Nulli-tetrasomic and di-telosomic analysis revealed the presence of three low seed size QTL-associated markers on three chromosomes, 6BL, 2DL, and 1DS respectively. This study clearly demonstrates that ISSRs are highly useful for finding markers associated with major and minor genes controlling agronomically important traits in wheat.

Genetic analysis of kernel hardness in bread wheat using PCR-based markers

Abstract In wheat, kernel hardness is a complex genetic trait involving various directly and indirectly contributing components such as kernel hardness per se, protein content, hectolitre weight and 1,000-kernel weight. In an attempt to identify DNA markers associated with this trait, 100 recombinant inbred lines (RILs) derived from a cross between a hard grain land-race, NP4, and a soft grain variety, HB 208, were screened with 100 ISSR and 360 RAPD primers. Eighteen markers were assigned to seven linkage groups covering 223.6 cM whereas 11 markers remained unlinked. A multiple-marker model explained the percentage of phenotypic variation for kernel hardness as 20.6%, whereas that for protein content, hectolitre weight and 1,000-kernel weight was 18.8%, 13.5% and 12.1%, respectively. Our results indicate that phenotypic expression of kernel hardness is controlled by many QTLs and is interdependent on various related traits.

Arbitrarily primed-PCR based diversity assessment reflects hierarchical groupings of Indian tetraploid wheat genotypes

Abstract Genetic diversity analysis using PCR with arbitrary decamer primers (RAPD — random amplified polymorphic DNA) was carried out in a set of 63 tetraploid wheat genotypes which comprised 24 durum landraces, 18 durum cultivars, nine dicoccum cultivars, ten less commonly cultivated species and two wild tetraploid species. The durum and dicoccum wheat genotypes are a part of the germplasm used in Indian tetraploid wheat breeding programs. A total of 206 amplification products were obtained with 21 informative primers, of which 162 were polymorphic. The highest degree of polymorphism was seen in the wild and less commonly cultivated species (68.9%). Durum released cultivars showed greater polymorphism (50.6%) than landraces (44.8%), while dicoccum cultivars showed a considerably low level of polymorphism (23.6%). Cluster analysis led to the separation of wild and cultivated genotypes, and among cultivated emmer wheat distinct groups were formed by the durum cultivars, durum landraces and dicoccum cultivars. The subgroupings of landraces had no relation to their geographical distribution. The durum cultivars formed subgroups based on common parentage in their pedigree. Among species, wild timopheevi wheat (T. araraticum) and its cultivated form (T. timopheevi) formed a distinct group distant from all other genotypes. The present study is a first attempt at determining the genetic variation in Indian tetraploid wheats at the molecular level.

Molecular Marker Analysis of Protein Content Using PCR-Based Markers in Wheat

Grain protein concentration (GPC) of hexaploid wheat is one of the important factors that determines the end-product quality, as well as playing a pivotal role in human nutrition. In an attempt to identify PCR-based DNA markers linked to GPC, 106 recombinant inbred lines (RILs) were developed from a cross between two wheat cultivars PH132 and WL711, which differ significantly in GPC, by the single seed descent method. The RILs were phenotyped for GPC at two diverse agroclimatic locations, namely Pune and Ludhiana, to study the influence of genotype and environment interactions on this trait. The parents were screened with 85 inter simple sequence repeat (ISSR) primers and 350 random primers. The selective genotyping and whole population analysis revealed nine DNA markers associated with the trait. Three markers (UBC8441100, UBC8801100, and OPA4800) were observed to be associated with the trait in both locations, whereas two markers (OPH41400 and UBC873750) were found to be specific to Pune, and four markers (OPM5870, OPO10870, OPV141200, and UBC8251000) were specific to Ludhiana. Together five markers at the Pune location representing five QTLs and seven markers at Ludhiana representing four QTLs accounted for 13.4 and 13.5% of total phenotypic variation, respectively. This study clearly demonstrates that GPC is highly influenced by the environment, and the applicability of ISSR and RAPD markers in finding regions on chromosomes associated with quantitative characters in wheat such as GPC.

Inheritance of β-carotene concentration in durum wheat (Triticum turgidum L. ssp. durum)

Despite being one of the important characteristics in determining pasta quality in durum wheat (Triticum turgidum ssp. durum), there is no direct report on inheritance of β-carotene concentration. The objectives of this study were to determine the inheritance of β-carotene concentration and the number of genes involved in six crosses of durum. For the cross PDW-233 (P1) × Bhalegaon-4 (P2), F1, F2, BCP1 and BCP2 populations were developed. For all other crosses, only the F1 and F2 populations were developed. β-carotene concentration was determined for all populations and parents of each cross grown at Hol, Maharastra, India. The cross PDW-233 × Bhalegaon-4 was also evaluated at Dharwad, Karnataka, India. Low β-carotene concentration was partially dominant in most of the crosses. Broad sense heritability was 67 and 91% at Dharwad and Hol, respectively, for the cross PDW-233 × Bhalegaon-4 and varied from 74 to 93% for the other five crosses indicating the presence of additive gene effects. The frequency distributions of the trait in the F2 populations were not normal and were skewed towards the lower parent. Segregation of β-carotene concentration in the six F2 populations indicated that at least two major genes and two or three minor genes with modifying effects govern the trait. Analysis of variance indicated that environment had comparatively little influence on the trait and this should allow for easy selection. The joint scaling test revealed additive × additive, additive × dominance and dominance × dominance epistatic interactions in the cross PDW-233 × Bhalegaon-4.

Inheritance and identification of DNA markers associated with yellow berry tolerance in wheat (Triticum aestivum L.)

Yellow berry (YB) is a serious seed disorder in durum wheat, bread wheatand triticale, which arises due to deficiency in nitrogen concentration in thesoil. YB seriously affects the grain protein content (GPC) thereby affectingbread making quality in bread wheat and pasta making quality in durumwheat. In order to study the inheritance and to identify DNA markersassociated with YB tolerance, a recombinant inbred line (RIL) populationof 113 individuals was developed by making a cross between RyeSelection111 (RS111), highly resistant to YB and Chinese Spring (CS), asusceptible parent. Phenotyping of this population to YB incidenceindicated that, at least one major gene/QTL and few minor genes governthe tolerance to YB. DNA marker analysis revealed linkage of twomicrosatellite markers Xgwm174 and Xgwm190 from chromosome 5Dwith YB tolerance while one ISSR marker UBC842600 and oneRAPD marker OPR81000 from chromosome 6B were found to beassociated with YB tolerance in repulsion phase. Association of YBtolerance with that of GPC was analyzed using the markers associated withYB tolerance. It was found to be reciprocal in this population in accordancewith the previous reports.

Note: Diversity Analysis of Indian Tetraploid Wheat Using Intersimple Sequence Repeat Markers Reveals Their Superiority over Random Amplified Polymorphic DNA Markers

Intersimple sequence repeat polymorphism (ISSR, Zietkiewicz et al., 1994) has emerged as a relatively new, reliable, and speedy marker system for germplasm evaluation and has been used in wheat for detection of polymorphism (Nagaoka and Ogihara, 1997), genetic mapping (Kojima et al., 1998) and tagging of quantitative traits (Ammirajuet al., in press) and in various other plants such as conifers (Tsumuraet al., 1996), citrus (Fanget al., 1997), grapevine (Moreno et al., 1998), and rice (Joshi et al., 2000) for assessment of variability in germplasm. In the present work, we have employed ISSR markers to characterize the variability in a set of Indian tetraploid wheat germplasm, which had been analyzed using RAPD markers in an earlier work by us (Pujar et al., 1999), and have compared the two marker systems for their suitability in the evaluation of tetraploid wheats.

An assessment of cultivated emmer germplasm for gluten proteins

The storage protein composition of 61 accessions of Triticum dicoccum was analyzed by SDS-PAGE (HMW- and LMW-glutenin subunits) and Acid-PAGE (gliadins). In the HMW-glutenin subunits, four allelic variants at the Glu-A1 and eight at the Glu-B1 locus were detected resulting in a total of 17 patterns. The Glu-B1 locus was found to be more polymorphic than the Glu-A1 locus. Interestingly, the presence of HMW subunits like 13+16, 2∗ and 1 associated with good quality was observed. Three accessions were null for both the Glu-A1 and Glu-B1 loci. There was less variation for gliadins. Three different gamma gliadin fractions coded by Gli-B1 locus were detected and there were eight different LMW-B glutenin patterns at the Glu-3 loci. The variability can be used to improve the utility of this crop.