Development of genome-wide PCR-based markers from insertion, deletion and single nucleotide polymorphisms for closely related Japanese rice cultivars and identification of QTLs for the appearance of cooked rice and polished rice.
Appearance of rice grain is an important property, affecting its acceptance by consumers. Moreover, appearance is a complex characteristic involving many components, including glossiness and whiteness. The genetic bases for the glossiness of cooked rice and the whiteness of polished rice (WPR) were determined using 133 recombinant inbred lines (RILs) derived from a cross between two closely related cultivars from Hokkaido, Joiku462, with high glossiness and whiteness, and Yukihikari, an ancestor of Joiku462 with low glossiness and whiteness. Analyses identified 167 genome-wide InDel markers, five cleaved amplified polymorphic sequences (CAPS) and eight derived CAPS markers differentiating the parental lines. The glossiness area (GLA) and glossiness strength (GLS) of cooked rice and WPR were determined for RILs in two locations, Pippu and Sapporo, Hokkaido. Four QTLs were detected.qGLA10andqGLS9were detected on chromosomes 10 and 9, respectively, with both being significant at both geographic locations.qWPR1on chromosome 1 was significant at Pippu, andqWPR4on chromosome 4 was significant at Sapporo. The Joiku462 alleles at all QTLs increased each trait. The PCR-based markers flanking these four QTLs may be useful for improvement of GLA, GLS and WPR.
Department of Agro-Environmental Science, Obihiro University of Agriculture and Veterinary Medicine , Nishi 2-11 Inada, Obihiro, Hokkaido 080-8555 , Japan.
Noriko
N
Kinoshita
Department of Agro-Environmental Science, Obihiro University of Agriculture and Veterinary Medicine , Nishi 2-11 Inada, Obihiro, Hokkaido 080-8555 , Japan.
Sho
S
Takano
Department of Agro-Environmental Science, Obihiro University of Agriculture and Veterinary Medicine , Nishi 2-11 Inada, Obihiro, Hokkaido 080-8555 , Japan.
Naomi
N
Shimoda
Graduate School of Agriculture, Hokkaido University , Kita 9 Nishi 9, Kita-ku, Sapporo, Hokkaido 060-8589 , Japan.
Itsuro
I
Takamure
Rice Breeding Group, Kamikawa Agricultural Experiment Station, Local Independent Administrative Agency Hokkaido Research Organization , Minami 1-5, Pippu, Hokkaido 078-0397 , Japan.
Takashi
T
Sato
Department of Agro-Environmental Science, Obihiro University of Agriculture and Veterinary Medicine , Nishi 2-11 Inada, Obihiro, Hokkaido 080-8555 , Japan.
Kiyoaki
K
Kato
CAPS marker; InDel marker; dCAPS marker; glossiness; whiteness