Near-isogenic lines carrying QTL for high spikelet number with the genetic background of IR64, an Indica-type rice variety


IR64, recognized globally as a high quality Indica-type rice variety, was first released by the International Rice Research Institute (IRRI) in 1985. To improve the yield potential of IR64, a set of near-isogenic lines (NILs) of IR64 with increased total spikelet number per panicle (TSN) was developed using New Plant Type (NPT) varieties as tropical Japonica-type donor parents.

A total of five NILs derived from different donor parents were developed through marker-assisted selection. Regardless of the donor parents, Quantitative Trait Locus (QTL) for high TSN was detected on common region of the long arm of chromosome 4 (Table 1, Fig. 1). We designated this QTL as qTSN4. Marker information linked to qTSN4 is shown in Table 1. NILs have 196-239 spikelets per panicle (i.e., 40-70% greater TSN than IR64), which is attributed to the increase in larger number of spikelets on the secondary and ternary rachis branches.  Variation in TSN was observed among NILs; the number of spikelets was greatest in IR64-NIL2 (IR65564-2-2-3 as donor parent) and in IR64-NIL4 (IR66215-44-2-3 as donor parent).

In this study, we succeeded in developing five NILs for high TSN with a rice variety (IR64) genetic background by employing molecular marker-assisted selection. The materials are expected to be useful for enhancing the yield potential of rice varieties. These NILs are also available for understanding the genetic basis of TSN and the effects of single QTL/gene by testing it under different environmental conditions. Further investigation is required to determine if the variation in panicle architecture is simply due to the allelic effects or not.

Figure, table

  1. Fig.1. The location of QTLs for spikelet number per panicle on the long arm of chromosome 4.
  2. Table 1. Marker information on QTLs and panicle structure of IR64 and its NILs for high TSN
  3. Fig.2. Panicle architecture of IR64 and its NILs for increased spikelet number

Japan International Research Center for Agricultural Sciences Biological Resources and Post-harvest Division


Administration A

Research project

Development of agricultural technologies in developing countries to respond to climate change

Program name

Environment and Natural Resource Management

Term of research

FY 2012 (FY 2005-FY 2012)

Responsible researcher

Kobayashi Nobuya ( 農研機構 次世代作物開発研究センター )

Fujita Daisuke ( 農研機構 作物研究所 )

Tagle Analiza G. ( 国際稲研究所 )

Ebron Leodegario A. ( 国際稲研究所 )

Fukuta Yoshimichi ( 熱帯・島嶼研究拠点 )

Ishimaru Tsutomu ( 生物資源・利用領域 )

Publication, etc.

Fujita et al. (2012), Breeding Science. 62:18-26

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English PDF

2012_03_A4_en.pdf149.35 KB