Mapping of Genes for Cooking and Eating Qualities in Thai Jasmine Rice (KDML105)

Abstract

Thai jasmine rice, KDML 105, is known as the best quality rice. It is known not only for its aroma but also for its good cooking and eating qualities. Amylose content (AC), gel consistency (GC) and gelatinization temperature (GT) are important traits determining rice quality. A population of recombinant inbred lines (RIL) derived from KDML105 x CT9993 cross was used to study the genetic control of AC, GC and GT traits. A total of 191 markers were used in the linkage map construction. The 1605.3 cM linkage map covering nearly the whole rice genome was used for QTL (define QTL) analysis. Four QTLs for AC were detected on chromosomes 3, 4, 6 and 7. These QTLs accounted for 80% of phenotypic variation explained (PVE) in AC. The presence of one major gene as well as several modifiers was responsible for the expression of the trait. Two QTLs on chromosome 6 and one on chromosome 7 were detected for GC, which accounts for 57% of PVE. A single gene of major effect along with modifier genes controls GC from this cross. The QTLs in the vicinity of waxy locus were major contributors in the expression of AC and GC. The finding that the position of QTLs for AC and GC were near each other may reflect tight linkage or pleiotropy. Three QTLs were detected, one on chromosome 2 and two on chromosome 6, which accounted for 67% of PVE in GT. Just like AC and GC, one major gene and modifier genes governed the variation in GT resulting from the KDML105 x CT9993 cross. Breeding for cooking and eating qualities will largely rely on the preferences of the end users.

Understanding the Fragrance in Rice

“…A similar mutational event was also reported by [30] in an aromatic rice variety Kayeema, in a gene responsible for 2AP within the flanking regions of RM515 and SSRJ07 on the longer arm of chromosome 8. The development of an in silico physical map using four BAC of Nipponbare spanning within a region of 386 bp from RM515 to SSRJ07 suggested one BAC clone (clone AP004463) as most likely to be having the gene.…”

“…Recent advancements in plant science and availability of high density linkage maps and fully sequenced rice genome have provided better opportunities for plant scientists to look inside the secrets of aroma in rice. Since, 2AP was found as a key role player behind the presence and absence of desired popcorn like characteristic aroma in most of the aromatic rice cultivars, plant scientists were more dedicated in understanding the regulation and molecular basis of 2AP resulting in a number of appreciable attempts in the array of mapping the gene governing the 2AP synthesis in several varieties of aromatic rice such as Della, Azucena [24][25][26][27], Suyunuo [28,29], KDML105 [30], Kyeema [31] and Wuxiangxian. But, the varying level of 2AP among different aromatic rice verities and its expensive assay limited the mapping experiments.…”

Homology Modeling, Functional Annotation and Comparative Genome Analysis of GBSS Enzyme in Rice and Maize Genomes

“…Many scientists studied the genetic basis of waxy gene using different genetic mapping approaches (Lanceras et al, 2000;Fan et al, 2005;Tian et al, 2005). But little or no work was done to study its 3D structure.…”

Identification of QTLs for resistant starch and total alkaloid content in brown and polished rice

“…Gelatinization temperature was controlled by the ALK gene, which encodes a putative soluble starch synthase II-3 (Gao et al, 2011). Two QTLs on chromosome 6 and one on chromosome 7 were detected for gel consistency, which accounts for 57% of phenotypic variation explained, meanwhile the position of QTLs for amylose content and gel consistency being close to each other may reflect linkage or pleiotropy (Lanceras et al, 2000). Two QTLs (qPKV7.1, qHPV7.1, qCPV7.1, and qSBV7.1) on chromosome 7 with contributions ranging from -31.8 to 53.2% were found to have pleiotropy .…”