title: Discovery and mapping of genomic regions governing economically important traits of Basmati rice.
abstract: BACKGROUND
  Basmati rice, originated in the foothills of Himalayas, commands a premium price in the domestic and international markets on account of its unique quality traits. The complex genetic nature of unique traits of Basmati as well as tedious screening methodologies involved in quality testing have been serious constraints to breeding quality Basmati. In the present study, we made an attempt to identify the genomic regions governing unique traits of Basmati rice.
  
  
  RESULTS
  A total of 34 Quantitative Trait Loci (QTLs) for 16 economically important traits of Basmati rice were identified employing F(2), F(3) and Recombinant Inbred Line (RIL) mapping populations derived from a cross between Basmati370 (traditional Basmati) and Jaya (semi-dwarf rice). Out of which, 12 QTLs contributing to more than 15 % phenotypic variance were identified and considered as major effect QTLs. Four major effect QTLs coincide with the already known genes viz., sd1, GS3, alk1 and fgr governing plant height, grain size, alkali spreading value and aroma, respectively. For the remaining major QTLs, candidate genes were predicted as auxin response factor for filled grains, soluble starch synthase 3 for chalkiness and VQ domain containing protein for grain breadth and grain weight QTLs, based on the presence of non-synonymous single nucleotide polymorphism (SNPs) that were identified by comparing Basmati genome sequence with that of Nipponbare.
  
  
  CONCLUSIONS
  To the best of our knowledge, the current study is the first attempt ever made to carry out genome-wide mapping for the dissection of the genetic basis of economically important traits of Basmati rice. The promising QTLs controlling important traits in Basmati rice, identified in this study, can be used as candidates for future marker-assisted breeding.
authors: Institute of Biotechnology, Acharya NG Ranga Agricultural University, Rajendranagar, Hyderabad, 500030, AP, India. drvlnreddy@gmail.com.|Centre for DNA Fingerprinting and Diagnostics, Hyderabad, 500001, India. drvlnreddy@gmail.com.
authors: Lakshminarayana R
authors: LR
authors: Vemireddy
authors: Centre for DNA Fingerprinting and Diagnostics, Hyderabad, 500001, India.
authors: Sabahat
authors: S
authors: Noor
authors: Centre for DNA Fingerprinting and Diagnostics, Hyderabad, 500001, India. vsatya@cdfd.org.in.
authors: V V
authors: VV
authors: Satyavathi
authors: Institute of Biotechnology, Acharya NG Ranga Agricultural University, Rajendranagar, Hyderabad, 500030, AP, India.|Centre for DNA Fingerprinting and Diagnostics, Hyderabad, 500001, India.
authors: A
authors: A
authors: Srividhya
authors: Centre for DNA Fingerprinting and Diagnostics, Hyderabad, 500001, India.
authors: A
authors: A
authors: Kaliappan
authors: Centre for DNA Fingerprinting and Diagnostics, Hyderabad, 500001, India.
authors: Srn
authors: S
authors: Parimala
authors: Institute of Biotechnology, Acharya NG Ranga Agricultural University, Rajendranagar, Hyderabad, 500030, AP, India.
authors: Prathibha M
authors: PM
authors: Bharathi
authors: Institute of Biotechnology, Acharya NG Ranga Agricultural University, Rajendranagar, Hyderabad, 500030, AP, India.
authors: Dondapati A
authors: DA
authors: Deborah
authors: Centre for DNA Fingerprinting and Diagnostics, Hyderabad, 500001, India.|Indian Institute of Rice Research, Hyderabad, India.
authors: K V Sudhakar
authors: KV
authors: Rao
authors: Indian Institute of Rice Research, Hyderabad, India.
authors: N
authors: N
authors: Shobharani
authors: Institute of Biotechnology, Acharya NG Ranga Agricultural University, Rajendranagar, Hyderabad, 500030, AP, India.|Centre for DNA Fingerprinting and Diagnostics, Hyderabad, 500001, India.
authors: E A
authors: EA
authors: Siddiq
authors: Centre for DNA Fingerprinting and Diagnostics, Hyderabad, 500001, India.
authors: Javaregowda
authors: J
authors: Nagaraju
mesh_terms: D000688:Amylose / Q000378:metabolism; D002874:Chromosome Mapping / Q000379:methods*; D020090:Chromosome Segregation / Q000235:genetics; D018556:Crops, Agricultural / Q000191:economics* / Q000235:genetics*; D003433:Crosses, Genetic; D063990:Gene Ontology; D017343:Genes, Plant; D008040:Genetic Linkage; D005819:Genetic Markers; D023281:Genomics; D007178:Inbreeding; D008126:Lod Score; D018895:Microsatellite Repeats / Q000235:genetics; D009812:Odorants; D012275:Oryza / Q000033:anatomy & histology / Q000235:genetics*; D010641:Phenotype; D040641:Quantitative Trait Loci / Q000235:genetics; D019655:Quantitative Trait, Heritable; D015203:Reproducibility of Results; D017422:Sequence Analysis, DNA; D013696:Temperature
chemical_list: D005819:Genetic Markers; D000688:Amylose