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Rice Genomics and Genetics 2012, Vol.3, No.1, 1
-
7
http://rgg.sophiapublisher.com
1
Research Report Open Access
Analysis of Genetic Structure in the USDA Rice Mini-Core Collection Using the
SQUAMOSA Promoter-binding-like Gene Family
Juansheng Ren
1*
, Yuchao Yu
1,2*
, Fangyuan Gao
1
, Lihua Zeng
2
, Xianjun Lu
1
, Xianting Wu
1
, Wengui
Yan
3
, Guangjun Ren
1
1. Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610066, P.R. China
2. Sichuan Normal University, Chengdu, 610066, P.R. China
3. Dale Bumpers National Rice Research Center, United States Department of Agriculture-Agricultural Research Service (USDA-ARS), 2890 Highway 130
East, Stuttgart, AR 72160, USA
* The authors contributed equally to the work
Corresponding authors email:
guangjun61@sina.com;
Authors
Rice Genomics and Genetics, 2012, Vol.3, No.1 doi: 10.5376/rgg.2012.03.0001
Received: 16 Dec., 2011
Accepted: 17 Jan., 2012
Published: 20 Jan., 2012
This article was first published in Molecular Plant Breeding in Chinese, and here was authorized to transl ate and publish the paper in English under the terms of
Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly
cited.
Preferred citation for this article:
Ren et al., 2012, Analysis of Genetic Structure in the USDA Rice Mini-Core Collection Using the SQUAMOSA Promoter-binding-like Gene Family, Rice
Genomics and Genetics, Vol.3, No.1 1
-
7 (doi: 10.5376/rgg.2012.03.0001)
Abstract
The SQUAMOSA (SQUA) promoter-binding-like (
SPL
) gene family is a plant specific transcription factor family and
has many important biological functions. In this study, 19 pairs of primers were designed based on 19
Oryza sativa
L. SQUAMOSA
promoter-binding-like (
OsSPL
) gene sequences and used for a polymorphism analysis with 171 accessions as a set of the United
States Department of Agriculture (USDA) rice mini-core collection established in the US. This mini-core represents the core of 1 794
accessions and the entire collection of 18 412 accessions. In total, 140 bands were amplified, and 128 of them were polymorphic,
occupying a great majority (up to 91.4%) of the mini-core collection. The average number of alleles per locus was 7.4. The cluster
and principal coordinate analysis agreeably classified the 171 accessions into six subgroups (subgroups
Ⅰ-Ⅵ
), and those in the
same subgroup were distributed throughout similar geographical and ecological regions worldwide. Days to heading for subgroup
Ⅵ
was significantly greater than the overall mean. Similarly, the plant height for subgroup
Ⅱ
and spikelets per panicle for subgroups
Ⅰ
and
Ⅲ
were significantly different from the overall mean, respectively. Thus, the
OsSPL
genes were associated with the days to
heading, plant height and spikelets per panicle.
Keywords
Rice; SQUAMOSA promoter-binding-like (
SPL
) genes family; Germplasm; Core collection; Gene-trait association
Background
Rice is a staple food for nearly half of the world's
population, and there are more than 100 000 rice
varieties planted worldwide that provide almost
one-quarter of the global per capita energy (Sasaki,
2008). The main agronomic traits in rice, such as the
grain number per spike, 1 000
-
grain weight and tillering
ability, directly influence rice yield (Gao et al., 2007;
Wang et al., 2009; Yang et al., 2000; Miura et al.,
2010). The
SQUAMOSA
promoter binding protein-like
(
SPL
) gene family contains a highly conservative
DNA domain that is representative of families of
plant-specific transcription factors and participates in
the adjustment of flowering-time, the transition of
flower development, the initiation of leaf development
and other developmental processes (Birkenbihl et al.,
2005; Wang et al., 2008; Wang et al., 2009; Dai et al.,
2010; Miura et al., 2010; Jiao et al., 2010). The
Oryza
sativa
L.
SQUAMOSA
promoter binding protein-like
14 (
OsSPL14
) gene has been cloned and proved to
involve in controlling the tiller number in the vegetative
developmental stage, whereas elevated expression of
OsSPL14
in the reproductive developmental stage will
promote branching, which resulted in a reduction of
tiller number, an increased number of spikelets and
grains per panicle, a thickened haulm, increased
lodging resistance, and enhanced grain yields (Jiao et
al., 2010; Miura et al., 2010). There are 19
OsSPL
genes annotated in the Rice Genome Annotation Project
(http://rice.plantbiology.msu.edu/). And all 19 genes