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BMC Genomics. 2018 Apr 20;19(1):273. doi: 10.1186/s12864-018-4639-4.

Genomic regions responsible for seminal and crown root lengths identified by 2D & 3D root system image analysis.

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Institute of Crop Science, National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8518, Japan.
Department of Plant Breeding and Genetics, Cornell University, Ithaca, NY, 14853, USA.
Department of Global Agricultural Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi, Bunkyo, Tokyo, 113-8657, Japan.
Robert W. Holley Center for Agriculture and Health, USDA-ARS, Cornell University, Ithaca, NY, 14853, USA.
Department of Plant Breeding and Genetics, Cornell University, Ithaca, NY, 14853, USA.
Global Institute for Food Security, University of Saskatchewan, Saskatoon, Canada.



Genetic improvement of root system architecture is a promising approach for improved uptake of water and mineral nutrients distributed unevenly in the soil. To identify genomic regions associated with the length of different root types in rice, we quantified root system architecture in a set of 26 chromosome segment substitution lines derived from a cross between lowland indica rice, IR64, and upland tropical japonica rice, Kinandang Patong, (IK-CSSLs), using 2D & 3D root phenotyping platforms.


Lengths of seminal and crown roots in the IK-CSSLs grown under hydroponic conditions were measured by 2D image analysis (RootReader2D). Twelve CSSLs showed significantly longer seminal root length than the recurrent parent IR64. Of these, 8 CSSLs also exhibited longer total length of the three longest crown roots compared to IR64. Three-dimensional image analysis (RootReader3D) for these CSSLs grown in gellan gum revealed that only one CSSL, SL1003, showed significantly longer total root length than IR64. To characterize the root morphology of SL1003 under soil conditions, SL1003 was grown in Turface, a soil-like growth media, and roots were quantified using RootReader3D. SL1003 had larger total root length and increased total crown root length than did IR64, although its seminal root length was similar to that of IR64. The larger TRL in SL1003 may be due to increased crown root length.


SL1003 carries an introgression from Kinandang Patong on the long arm of chromosome 1 in the genetic background of IR64. We conclude that this region harbors a QTL controlling crown root elongation.


Chromosome segment substitution line (CSSL); Image processing; Oryza sativa; QTL; Root phenotyping; Root system architecture

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