Genetic control of soybean seed oil: I. QTL and genes associated with seed oil concentration in RIL populations derived from crossing moderately high-oil parents

Soybean seed is a major source of oil for human consumption worldwide and the main renewable feedstock for biodiesel production in North America. Increasing seed oil concentration in soybean [Glycine max (L.) Merrill] with no or minimal impact on protein concentration could be accelerated by exploiting quantitative trait loci (QTL) or gene-specific markers. Oil concentration in soybean is a polygenic trait regulated by many genes with mostly small effects and which is negatively associated with protein concentration. The objectives of this study were to discover and validate oil QTL in two recombinant inbred line (RIL) populations derived from crosses between three moderately high-oil soybean cultivars, OAC Wallace, OAC Glencoe, and RCAT Angora. The RIL populations were grown across several environments over 2 years in Ontario, Canada. In a population of 203 F_3:6 RILs from a cross of OAC Wallace and OAC Glencoe, a total of 11 genomic regions on nine different chromosomes were identified as associated with oil concentration using multiple QTL mapping and single-factor ANOVA. The percentage of the phenotypic variation accounted for by each QTL ranged from 4 to 11 %. Of the five QTL that were tested in a population of 211 F_3:5 RILs from the cross RCAT Angora × OAC Wallace, a “trait-based” bidirectional selective genotyping analysis validated four QTL (80 %). In addition, a total of seven two-way epistatic interactions were identified for oil concentration in this study. The QTL and epistatic interactions identified in this study could be used in marker-assisted introgression aimed at pyramiding high-oil alleles in soybean cultivars to increase oil concentration for biodiesel as well as edible oil applications.     

Mapping and validation of simple sequence repeat markers linked to a major gene controlling seed cadmium accumulation in soybean [Glycine max (L.) Merr]

Daily consumption of cadmium (Cd) contaminated foods poses a risk to human health. Cultivar selection is an important method to limit Cd uptake and accumulation, however, analyzing grain Cd concentration is costly and time-consuming. Developing markers for low Cd accumulation will facilitate marker assisted selection (MAS). Inheritance studies using a threshold value of 0.2 mg kg^?1 for low and high and an F_2:3 population showed that low Cd accumulation in soybean seed is under the control of a major gene (Cda1, proposed name) with the allele for low accumulation being dominant. A recombinant inbred line (RIL) population (F_6:8) derived from the cross AC Hime (high Cd accumulation) and Westag-97 (low Cd accumulation) was used to identify the DNA markers linked to Cda gene(s) or quantitative trait loci (QTLs) controlling low Cd accumulation. We screened 171 simple sequence repeat (SSR) primers that showed polymorphism between parents on the 166 RILs. Of these, 40 primers were newly developed from the soybean genomic DNA sequence. Seven SSR markers, SatK138, SatK139, SatK140 (0.5 cM), SatK147, SacK149, SaatK150 and SattK152 (0.3 cM), were linked to Cda1 in soybean seed. All the linked markers were mapped to the same linkage group (LG) K. The closest flanking SSR markers linked to Cda1 were validated using a parallel population (RILs) involving Leo × Westag-97. Linked markers were also validated with diverse soybean genotypes differing in their seed Cd concentration and showed that SSR markers SatK147, SacK149, and SattK152 clearly differentiated the high and low Cd accumulating genotypes tested. To treat Cd uptake as a quantitative trait, QTL analysis using a linkage map constructed with 161 markers identified a major QTL associated with low Cd concentration in the seeds. The QTL was also mapped to the same location as Cda1 on LG-K. This QTL accounted for 57.3% of the phenotypic variation. Potential candidate genes (genes with known or predicted function that could influence the seed Cd concentration) like protein kinase, putative Adagio-like protein, and plasma membrane H⁺-ATPase were found to be located in the locus of interest. Of the four SSR markers located in the region, SattK152 was localized in the plasma membrane H⁺-ATPase gene. SSR markers closely linked to Cda1 in seeds of soybean were identified and have potential to be used for MAS to develop low Cd accumulating cultivars in a breeding program.     

Construction of an RAPD linkage map and localization of QTLs for oleic acid level using recombinant inbreds in mustard (Brassica juncea).

RAPD markers were employed for construction of a linkage map and localization of QTLs for oleic acid level using a set of 94 recombinant inbred lines (RILs) of mustard (Brassica juncea L.) as a mapping population. Only 30% of the 235 random primers used were useful in terms of polymorphism detected and the reproducibility of those patterns. Normal Mendelian segregation was observed for the majority of the 130 markers obtained with 71 informative primers; only 13.1% deviated (P < 0.01) from the expected 1:1 ratio. One-hundred and fourteen markers were assigned to 21 linkage groups (LGs) covering a total length of 790.4 cM with an average distance of 6.93 cM between markers. Two quantitative trait loci (QTL) for oleic acid level were mapped to 14- and 10.6-cM marker intervals on two different LGs. Both loci together explained 32.2% of phenotypic variance. One major QTL explained 28.5% of the trait variance observed in this species.     

Genotypic variation and identification of QTLs for agronomic traits,using AFLP and SSR markers in RILs of sunflower (<Emphasis Type="Italic">Helianthus annuus</Emphasis> L.)

A population of 77 recombinant inbred lines (RILs) were developed through single-seed descent from a cross between PAC-2 and RHA-266. Seeds of the above-mentioned RILs and their parents were planted in the field in a randomised complete block design with two replications. Genetic control for some agronomical traits—sowing-to-flowering date, plant height, stem diameter (SD), head diameter (HD), grain weight per plant, 1,000-grain weight (TGW) and the percentage of oil in grains—were measured for RILs and their parents. Genetic variability was observed among 77 RILs for all traits studied. Transgressive segregation occurred for some traits, and the comparison between 10% of selected RILs with the best parent showed significant difference for SD and HD as well as for TGW. A set of 123 RILs from the same cross, including the 77 above-mentioned RILs and their two parents, were screened with 409 AFLP and SSR markers, and a linkage map was constructed based on 367 markers. Several QTLs associated with the studied traits were identified. The effects of each QTL are moderate, ranging from 7% to 37%, but a high percentage of phenotypic variance is explained when considering all the covariants (TR² mean around 80% in each trait). Although the detected regions need to be more precisely mapped, the information obtained should help in marker-assisted selection.     

Molecular Mapping of Loci Affecting the Contents of Three Major Fatty Acids in Indian Mustard (Brassica juncea L)

The fatty acid constituents of mustard oil are palmitic, stearic, oleic, linoleic, linolenic and erucic acids. With the objective of mapping loci influencing the content of these fatty acids, a population of F₆ generation recombinant inbred lines (RILs) derived from an inter-varietal cross of mustard was analyzed. Transgressive variation was evident for all the six fatty acids analysed irrespective of the levels of differences between the parents. The frequency distribution was normal for the linolenic acid, linoleic acid and stearic acid contents, while deviation from normality was observed for the other three fatty acids. The content of erucic acid was negatively correlated with the contents of all other fatty acids, which were positively correlated. Based on single marker analysis and interval mapping, two loci each for linoleic, linolenic and erucic acids were mapped to marker intervals on three linkage groups. Position of log of odds ratio (LOD) peaks suggested presence of common, linked and independently segregating loci for the fatty acid contents. The percentage of phenotypic variance explained by individual quantitative trait loci (QTLs) ranged from 10.5 to 19.5%, whereas the cumulative action of loci detected for different traits accounted for 16.3 to 27.6% of the variance. The additive effect for an individual locus ranged from 1.09 to 4.33. Presence of the favourable alleles at both the contributing loci in most of the RILs with a high linolenic acid content and of the unfavourable alleles in the lines with a low linolenic acid content indicated the possibility of pyramiding useful genes from phenotypically similar parental lines.     

RAPD-based SCAR marker SCA 12 linked to recessive gene conferring resistance to anthracnose in sorghum [Sorghum bicolor (L.) Moench]

Anthracnose, caused by Colletotrichum graminicola, infects all aerial parts of sorghum, Sorghum bicolor (L.) Moench, plants and causes loss of as much as 70%. F₁ and F₂ plants inoculated with local isolates of C. graminicola indicated that resistance to anthracnose in sorghum accession G 73 segregated as a recessive trait in a cross with susceptible cultivar HC 136. To facilitate the use of marker-assisted selection in sorghum breeding programs, a PCR-based specific sequence characterized amplified region (SCAR) marker was developed. A total of 29 resistant and 20 susceptible recombinant inbred lines (RILs) derived from a HC 136 × G 73 cross was used for bulked segregant analysis to identify a RAPD marker closely linked to a gene for resistance to anthracnose. The polymorphism between the parents HC 136 and G 73 was evaluated using 84 random sequence decamer primers. Among these, only 24 primers generated polymorphism. On bulked segregant analysis, primer OPA 12 amplified a unique band of 383 bp only in the resistant parent G 73 and resistant bulk. Segregation analysis of individual RILs showed the marker OPA 12₃₈₃ was 6.03 cM from the locus governing resistance to anthracnose. The marker OPA 12₃₈₃ was cloned and sequenced. Based on the sequence of cloned RAPD product, a pair of SCAR markers SCA 12-1 and SCA 12-2 was designed using the MacVector program, which specifically amplified this RAPD fragment in resistant parent G 73, resistant bulk and respective RILs. Therefore, it was confirmed that SCAR marker SCA 12 is at the same locus as RAPD marker OPA 12₃₈₃ and hence, is linked to the gene for resistance to anthracnose.     

Identification of the chromosomal region responsible for high-temperature stress tolerance during the grain-filling period in rice

An unusually high temperature during the grain-filling period, such as that caused by global warming, impairs the quality of rice (Oryza sativa L.) grains. This sensitivity to high-temperature stress is different among cultivars, suggesting the possibility of developing a high-temperature-tolerant cultivar. Since marker-assisted selection would reduce time and labor in breeding for such a quantitative trait, we determined the chromosomal region responsible for high-temperature tolerance during the grain-filling period. A high-temperature-sensitive japonica cultivar Tohoku 168 and a tolerant japonica cultivar Kokoromachi were selected as the parental lines of recombinant inbred lines (RILs) by high-temperature stress treatment from 5 to 10 days after anthesis, which was found to be the period most critical for grain quality. Using the RILs, whose genotypes were determined by analysis with 131 DNA markers which were selected as polymorphic markers between these two cultivars from 2,648 DNA markers tested, the quantitative trait locus (QTL) for the percentage of white-back grains was mapped on chromosome 6. The Kokoromachi allele of the QTL, which had a positive additive effect on the high-temperature tolerance, was introduced into the Tohoku 168 genome by repeated backcrossings with marker-assisted selection. Using high-temperature stress treatment of the near isogenic lines developed, the QTL on chromosome 6 was localized within a 1.9-Mb region between two DNA markers, ktIndel001 and RFT1. These DNA markers would be useful not only for breeding high-temperature-tolerant cultivars but also for map-based cloning of the QTL.     

Design of New Genome- and Gene-Sourced Primers and Identification of QTL for Seed Oil Content in a Specially High-Oil Brassica napus Cultivar

Rapeseed (Brassica napus L.) is one of most important oilseed crops in the world. There are now various rapeseed cultivars in nature that differ in their seed oil content because they vary in oil-content alleles and there are high-oil alleles among the high-oil rapeseed cultivars. For these experiments, we generated doubled haploid (DH) lines derived from the cross between the specially high-oil cultivar zy036 whose seed oil content is approximately 50% and the specially low-oil cultivar 51070 whose seed oil content is approximately 36%. First, to address the deficiency in polymorphic markers, we designed 5944 pairs of newly developed genome-sourced primers and 443 pairs of newly developed primers related to oil-content genes to complement the 2244 pairs of publicly available primers. Second, we constructed a new DH genetic linkage map using 527 molecular markers, consisting of 181 publicly available markers, 298 newly developed genome-sourced markers and 48 newly developed markers related to oil-content genes. The map contained 19 linkage groups, covering a total length of 2,265.54 cM with an average distance between markers of 4.30 cM. Third, we identified quantitative trait loci (QTL) for seed oil content using field data collected at three sites over 3 years, and found a total of 12 QTL. Of the 12 QTL associated with seed oil content identified, 9 were high-oil QTL which derived from the specially high-oil cultivar zy036. Two high-oil QTL on chromosomes A2 and C9 co-localized in two out of three trials. By QTL mapping for seed oil content, we found four candidate genes for seed oil content related to four gene markers: GSNP39, GSSR161, GIFLP106 and GIFLP046. This information will be useful for cloning functional genes correlated with seed oil content in the future.     

Identification of <Emphasis Type="Italic">qSOR1</Emphasis>, a major rice QTL involved in soil-surface rooting in paddy fields

Specific Indonesian lowland rice (Oryza sativa L.) cultivars elongate thick primary roots on the soil surface of paddy fields. To clarify the genetic factors controlling soil-surface rooting, we performed quantitative trait locus (QTL) analyses using 124 recombinant inbred lines (RILs) derived from a cross between Gemdjah Beton, an Indonesian lowland rice cultivar with soil-surface roots, and Sasanishiki, a Japanese lowland rice cultivar without soil-surface roots. These cultivars and the RILs were tested for soil-surface rooting in a paddy field. We identified four regions of chromosomes 3, 4, 6, and 7 that were associated with soil-surface rooting in the field. Among them, one major QTL was located on the long arm of chromosome 7. This QTL explained 32.5–53.6% of the total phenotypic variance across three field evaluations. To perform fine mapping of this QTL, we measured the basal root growth angle of crown roots at the seedling stage in seven BC₂F₃ recombinant lines grown in small cups in a greenhouse. The QTL was mapped between markers RM21941 and RM21976, which delimit an 812-kb interval in the reference cultivar Nipponbare. We have designated this QTL qSOR1 (quantitative trait locus for SOIL SURFACE ROOTING 1).     

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

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. Received: 25 July 2000 / Accepted: 24 November 2000     

Construction of a Genetic Linkage Map and Identification of QTLs for Seed Weight and Seed Size Traits in Lentil (Lens culinaris Medik.)

Seed weight and seed size both are quantitative traits and have been considered as important components of grain yield, thus identification of quantitative trait loci (QTL) for seed traits in lentil (Lens culinaris) would be beneficial for the improvement of grain yield. Hence the main objective of this study was to identify QTLs for seed traits using an intraspecific mapping population derived from a cross between L. culinaris cv. Precoz (seed weight-5.1g, seed size-5.7mm) and L. culinaris cv. L830 (seed weight-2.2g, seed size-4mm) comprising 126 F₈-RILs. For this, two microsatellite genomic libraries enriched for (GA/CT) and (GAA/CTT) motif were constructed which resulted in the development of 501 new genomic SSR markers. Six hundred forty seven SSR markers (including 146 previously published) were screened for parental polymorphism and 219 (33.8%) were found to be polymorphic among the parents. Of these 216 were mapped on seven linkage groups at LOD4.0 spanning 1183.7cM with an average marker density of 5.48cM. Phenotypic data from the RILs was used to identify QTLs for the seed weight and seed size traits by single marker analysis (SMA) followed by composite interval mapping (CIM) which resulted in one QTL each for the 2 traits (qSW and qSS) that were co-localized on LG4 and explained 48.4% and 27.5% of phenotypic variance respectively. The current study would serve as a strong foundation for further validation and fine mapping for utilization in lentil breeding programs.     

QTL mapping of slow-rusting, adult plant resistance to race Ug99 of stem rust fungus in PBW343/Muu RIL population

Races of stem rust fungus pose a major threat to wheat production worldwide. We mapped adult plant resistance (APR) to Ug99 in 141 lines of a PBW343/Muu recombinant inbred lines (RILs) population by phenotyping them for three seasons at Njoro, Kenya in field trials and genotyping them with Diversity Arrays Technology (DArT) markers. Moderately susceptible parent PBW343 and APR parent Muu displayed mean stem rust severities of 66.6 and 5 %, respectively. The mean disease severity of RILs ranged from 1 to 100 %, with an average of 23.3 %. Variance components for stem rust severity were highly significant (p < 0.001) for RILs and seasons and the heritability (h ²) for the disease ranged between 0.78 and 0.89. Quantitative trait loci (QTL) analysis identified four consistent genomic regions on chromosomes 2BS, 3BS, 5BL, and 7AS; three contributed by Muu (QSr.cim-2BS, QSr.cim-3BS and QSr.cim-7AS) and one (QSr.cim-5BL) derived from PBW343. RILs with flanking markers for these QTLs had significantly lower severities than those lacking the markers, and combinations of QTLs had an additive effect, significantly enhancing APR. The QTL identified on chromosome 3BS mapped to the matching region as the known APR gene Sr2. Four additional QTLs on chromosomes 1D, 3A, 4B, and 6A reduced disease severity significantly at least once in three seasons. Our results show a complex nature of APR to stem rust where Sr2 and other minor slow rusting resistance genes can confer a higher level of resistance when present together.     

Mapping of quantitative trait loci for oil content in cottonseed kernel

Oil content in cottonseed is a major quality trait which when improved through breeding could enhance the competitiveness of cottonseed oil among other vegetable oils. Cottonseed oil content is a quantitative trait controlled by genes in the tetraploid embryo and tetraploid maternal plant genomes, and the knowledge of quantitative trait loci (QTLs) and the genetic effects related to oil content in both genomes could facilitate the improvement in its quality and quantity. However, till date, QTL mapping and genetic analysis related to this trait in cotton have only been conducted in the tetraploid embryo genome. In the current experiment, an IF₂ population of cottonseed kernels from the random crossing of 188 intraspecific recombinant inbred lines which were derived from the hybrid of two parents, HS46 and MARCABUCAG8US-1-88, were used to simultaneously locate QTLs for oil content in the embryo and maternal plant genomes. The four QTLs found to be associated with oil content in cottonseed were: qOC-18-1 on chromosome 18; qOC-LG-11 on linkage group 11; qOC-18-2 on chromosome 18; and qOC-22 on chromosome 22. At a high selection threshold of 0.05, there was strong evidence linking the QTLs above the oil content in cottonseed. Embryo additive and dominant effects from the tetraploid embryo genome, as well as maternal additive effects from the tetraploid maternal plant genome were found to be significant contributors to genetic variation in cottonseed oil content.     

AFLP mapping of QTLs for in vitro organogenesis traits using recombinant inbred lines in sunflower (Helianthus annuus L.)

Genetic control for two in vitro organogenesis traits, the number of shoots per explant plated (S/E) and the number of shoots per regenerating explant (S/RE), was investigated in 75 recombinant inbred lines (RILs) of sunflower and their two parents (PAC-2 and RHA-266). Genetic variability was observed among the 75 RILs for the organogenesis traits studied. Some RILs presented significant differences when compared with the best parental line (RHA-266). Genetic gain, in terms of the percentage of the best parent, for 32% of the selected RILs was significant. A set of 99RILs from the same cross including the 75 mentioned above was screened with 333 AFLP markers and a linkage map was constructed based on 264 linked loci. Six putative QTLs for the S/RE (tentatively named osr) and seven QTLs for the S/E (ose) trait were detected using composite interval mapping. For each trait, the QTLs explained 52% (ose) and 67% (osr) of the total phenotypic variance. These results suggested that additive gene effects predominate in explaining a large proportion of the observed genetic variation associated with regeneration ability. The coincidental location of QTLs for S/E and S/RE is discussed. Received: 20 September 1999 / Accepted: 16 May 2000     

QTL Mapping of Leafy Heads by Genome Resequencing in the RIL Population of Brassica rapa

Leaf heads of cabbage (Brassica oleracea), Chinese cabbage (B. rapa), and lettuce (Lactuca sativa) are important vegetables that supply mineral nutrients, crude fiber and vitamins in the human diet. Head size, head shape, head weight, and heading time contribute to yield and quality. In an attempt to investigate genetic basis of leafy head in Chinese cabbage (B. rapa), we took advantage of recent technical advances of genome resequencing to perform quantitative trait locus (QTL) mapping using 150 recombinant inbred lines (RILs) derived from the cross between heading and non-heading Chinese cabbage. The resequenced genomes of the parents uncovered more than 1 million SNPs. Genotyping of RILs using the high-quality SNPs assisted by Hidden Markov Model (HMM) generated a recombination map. The raw genetic map revealed some physical assembly error and missing fragments in the reference genome that reduced the quality of SNP genotyping. By deletion of the genetic markers in which recombination rates higher than 20%, we have obtained a high-quality genetic map with 2209 markers and detected 18 QTLs for 6 head traits, from which 3 candidate genes were selected. These QTLs provide the foundation for study of genetic basis of leafy heads and the other complex traits.     

Fine mapping a major QTL <Emphasis Type="Italic">qFCC7</Emphasis><Subscript><Emphasis Type="Italic">L</Emphasis></Subscript> for chlorophyll content in rice (<Emphasis Type="Italic">Oryza sativa</Emphasis> L.) cv. PA64s

Chlorophyll (Chl) content is an important agronomic trait directly affecting the photosynthetic rate. Using a high-density genetic map of 132 recombinant inbred lines (RILs) derived from the cross between 93-11 and PA64s, we detected the quantitative trait loci (QTLs) for Chl content of the top three leaves under two nitrogen (N) conditions at two developmental stages. A total of 32 main-effect QTLs located on chromosomes 1, 4, 5, 6, 7, 8, and 12 were identified, and these QTLs individually accounted for 6.0–20.8?% of the total phenotypic variation. A major QTL qFCC7 _L affecting the Chl content under low N condition was identified, and its positive allele came from PA64s. This QTL might be associated with the ability to tolerate low-N stress in rice. The chromosomal segment substitution line (CSSL) with the corresponding segment from PA64s had a higher SPAD value and photosynthetic rate than 93-11 and showed a lower specific leaf area (SLA). We performed a fine-mapping using a BC₄F₂ population via marker-assisted backcross and finally mapped this QTL to a 124.5 kb interval on the long arm of chromosome 7. Candidate gene analysis showed that there were sequence variations and expression differences in the predicted candidate gene between the two parents. These results suggest that the QTL qFCC7 _L may be useful for breeding the rice varieties with higher photosynthetic rate and grain yield.     

Restriction site polymorphism-based candidate gene mapping for seedling drought tolerance in cowpea [Vigna unguiculata (L.) Walp.]

Quantitative trait loci (QTL) studies provide insight into the complexity of drought tolerance mechanisms. Molecular markers used in these studies also allow for marker-assisted selection (MAS) in breeding programs, enabling transfer of genetic factors between breeding lines without complete knowledge of their exact nature. However, potential for recombination between markers and target genes limit the utility of MAS-based strategies. Candidate gene mapping offers an alternative solution to identify trait determinants underlying QTL of interest. Here, we used restriction site polymorphisms to investigate co-location of candidate genes with QTL for seedling drought stress-induced premature senescence identified previously in cowpea. Genomic DNA isolated from 113 F_2:8 RILs of drought-tolerant IT93K503-1 and drought susceptible CB46 genotypes was digested with combinations of EcoR1 and HpaII, Mse1, or Msp1 restriction enzymes and amplified with primers designed from 13 drought-responsive cDNAs. JoinMap 3.0 and MapQTL 4.0 software were used to incorporate polymorphic markers onto the AFLP map and to analyze their association with the drought response QTL. Seven markers co-located with peaks of previously identified QTL. Isolation, sequencing, and blast analysis of these markers confirmed their significant homology with drought or other abiotic stress-induced expressed sequence tags (EST) from cowpea and other plant systems. Further, homology with coding sequences for a multidrug resistance protein 3 and a photosystem I assembly protein ycf3 was revealed in two of these candidates. These results provide a platform for the identification and characterization of genetic trait determinants underlying seedling drought tolerance in cowpea.     

Screening of IR50?×?Rathu Heenati F7 RILs and Identification of SSR Markers Linked to Brown Planthopper (Nilaparvata lugens St?l) Resistance in Rice (Oryza sativa L.)

Brown planthopper (Nilaparvata lugens St?l) is one of the major insect pests of rice. A Sri Lankan indica rice cultivar Rathu Heenati was found to be resistant to all biotypes of the brown planthopper. In the present study, a total of 268 F₇ RILs of IR50 and Rathu Heenati were phenotyped for their level of resistance against BPH by the standard seedbox screening test (SSST) in the greenhouse. A total of 53 SSR primers mapped on the chromosome 3 were used to screen the polymorphism between the parents IR50 and Rathu Heenati, out of which eleven were found to be polymorphic between IR50 and Rathu Heenati. The eleven primers that have shown polymorphism between the IR50 and Rathu Heenati parents were genotyped in a set of five resistant RILs and five susceptible RILs along with the parents for co-segregation analysis. Among the eleven primers, two primers namely RM3180 (18.22 Mb) and RM2453 (20.19 Mb) showed complete co-segregation with resistance. The identification of SSR markers linked with BPH resistant could be used for the maker assisted selection (MAS) program in rice breeding and to map the resistant genes on rice chromosomes for further gene cloning.     

Mapping and validation of a major QTL for yellow pigment content on 7AL in durum wheat (<Emphasis Type="Italic">Triticum turgidum</Emphasis> L. ssp. <Emphasis Type="Italic">durum</Emphasis>)

Yellow pigment content in durum wheat (Triticum turgidum L. ssp. durum) is an important criterion for both pasta bright yellow color and human health because of antioxidant properties of carotenoids involved in this pigmentation. In the present study, QTLs for yellow pigment content in durum wheat were mapped in a population of 140 RILs developed from a intraspecific cross between a released variety (PDW 233) and a landrace (Bhalegaon 4). This trait was evaluated in one location for 3 years and in two more locations for one additional year (five different year × location combinations further called “environments”). Yellow pigment content was highly heritable across the five different environments. Analysis of variance showed the significant effect of genotype, environment and genotype × environment interaction on the trait. Five different QTLs linked to yellow pigment content were identified on chromosome 1A, 3B, 5B, 7A and 7B across five different environments. The strongest one located on the distal part of the long arm of chromosome 7A, QYp.macs-7A, explained 55.22% of the variation in the trait, while, remaining four QTLs explained 5–8.75% of phenotypic variation in yellow pigment content. Marker analysis revealed significant association of one ISSR and one AFLP fragment with the trait. These two markers were linked to the major QTL QYp.macs-7A and were converted into SCAR markers. These SCAR markers were further validated on another population as well as 38 diverse genotypes so as to prove their potential in marker assisted selection. These markers will be very useful for the marker assisted breeding of durum wheat for higher yellow pigment content.     

Fine mapping of grain length QTLs on chromosomes 1 and 7 in Basmati rice (Oryza sativa L.)

Grain dimensions (length, breadth and length/breadth ratio) are important quality attributes of Basmati rice for its high consumer acceptance. Earlier we identified two significant quantitative trait loci (QTL) intervals on chromosomes 1 and 7 for grain dimensions in Basmati rice using a population of recombinant inbred lines (RILs) from cross between Basmati variety Pusa 1121 and a short grain non-aromatic variety Pusa 1342. For fine mapping of these QTLs, 184 F₆ RILs were grown and phenotyped in the normal rice growing season at two different locations. Forty-nine new SSR markers targeting these QTL intervals were tested and nine were found polymorphic between the parents. Using revised genetic maps adding new markers, the grain length QTL qGRL1.1 on chromosome 1 was narrowed down to 108?kbp from the earlier reported 6,133?kbp. There were total 13 predicted gene models in this interval which includes the probable candidate gene for the exceptionally high grain length of Basmati variety Pusa 1121. Similarly, two tandem QTL intervals qGRL7.1 and qGRL7.2 on chromosome 7 were merged into a single one narrowed down to 2,390?kbp from the earlier reported length of 5,269?kbp. This region of chromosome 7 also has co-localized QTLs for grain breadth and length to breadth ratio. SSR markers tightly linked to the QTL at a map distance of ??0.2?cM were developed for the qGRL1.1 and qGRL7.1 loci that could be used for marker-assisted breeding. Validation of earlier published markers for the grain length gene GS3 on chromosome 3 showed no difference between Pusa 1121 and Pusa 1342, highlighting the significance of qGRL1.1 and qGRL7.1 for the extra grain length of Basmati variety Pusa 1121.