A genetic diversity assessment of starch quality traits in rice landraces from the Taihu b

A genetic diversity assessment of starch quality traits in rice landraces from the Taihu basin,China

AO Yan1,2,XU Yong1,CUI Xiao-fen1,WANG An1,TENG Fei1,SHEN Li-qun1,LIU Qiao-quan1 1Key Laboratory of Crop Genetics and Physiology of Jiangsu Province/Co-Innovation Center for Modern Production Technology

of

Grain

Crops/College

of

Agriculture,Yangzhou

University,Yangzhou 225009,P.R.China2Suzhou Chien-Shiung Institute of Technology,Suzhou 215411,P.R.China 【期刊名称】农业科学学报（英文版） 【年(卷),期】2016(015)003 【总页数】9

【关键词】Keywords:

intragenic

molecular

marker,starch

synthesis,improved cultivars,cluster analysis,polymorphism information content Abstract

There are nearly 1 000 rice landrace varieties in the Taihu basin,China.To assess the genetic diversity of the rice,24 intragenic molecular markers（representing 17 starch synthesis-related genes）were investigated in 115 Taihu basin rice landraces and 87 improved cultivars simultaneously.The results show that the average genetic diversity and polymorphism information content values of the landraces were higher than those of improved cultivars.In total,41 and 39 allele combinations

（of the 17 genes）were derived from the landraces and improved cultivars,respectively; only two identical allele combinations were found bet ween the two rice variety sources.Cluster analysis,based on the molecular markers,revealed that the rice varieties could be subdivided into five groups and,within t hese,the japonica improved rice and japonica landrace rice varieties were in two separate groups.According to the quality reference criteria to classify the rice into grades,some of the landraces were found to perform we ll,in terms of starch quality.For example,according to NY/T595-2002 criteria from the Ministry of Agriculture of China,25 and 33 landraces reached grade 1,in terms of their apparent amylose content and gel consistency.Th e varieties that had outstanding quality could be used as breeding materials for rice quality breeding programs in the future.Our study is useful for future applications,such as genetic diversity studies,the protection of rice variety and improvment of rice quality in breeding programs. Received 6 February,2015 Accepted 10 April,2015 AO

Yan,Mobile: +86-18051236202,E-mail: 350685056@

LIU

Qiao-quan,Tel:

qq.com;

Correspondence qqliu@yzu.edu.cn

+86-514-87979242,E-mail:

? 2016,CAAS.All rights reserved.Published by Elsevier Ltd.

1.Introduction

Breeding success in crops is strongly related to the genetic variation of

the materials available,that is,the germplasm resources; an

understanding of the population structure and genetic variation in the germplasm is a prerequisite for crop genetic improvement（Xiao et al.2012）.Rice is one of the most important economic crops in China.However,a gradual reduction of th e genetic diversity of breeding varieties

could

hinder

future

breeding

programs.Thus,further

investigation into the genetic diversity of existing landraces is critical for the sustainable development of this economic crop.

Since the 1950s,the genetic diversity of the breeding varieties of rice has been decreasing（Qi et al.2006）.Lin andMin（1991）reported that several

common

rice

varieties

were

descendants

of

the

Aizizhan,Nantehao,Nongken 58,and Yinfangzhu varieties.Jin et al.（2006）found that the average similarity coefficient between rice varieties in the Taihu basin was 0.902.In fact,it is difficult to distinguish between the genotypes of several varieties of rice,such as Wuyunjing 7 and Wuyunjing 8.Continuous breeding programs have led to a trend of simplification in numerous agricultural crops,resulting in gene loss and a reducti on in genetic diversity（Donini et al.2000; Tian et al.2005）.Such narrow genetic bases pose potential risks to economic crop industries.

The Taihu basin is located at the juncture of Jiangsu,Zhejiang and Shanghai,between the lower reaches of the Yangtze River and

Hangzhou Bay.Local residents have been cultivating rice in the basin for over 8 000 years（Wang et al.2000）.Both natural evolution and artificial selection have contributed to the high diversity of rice present in the Taihu basin（Guo et al.1986; Jiang et al.1986）, including unique phenotypic,resistance

and

quality

characteristics.However,while

breeding programs to date have involved several local varieties,for example,Huangkezaonianri,Aininghuang and Laohu,numerous varieties have not been fully utilized as yet.

Improved living standards have raised expectations for high quality rice in many markets,facilitating an increase in research into rice quality traits in recent years.The quantity of starch in the endosperm of rice grains is a very important determinant of rice quality; it is essential to understand the genetic effects of starch synthesis-related genes in high-yielding rice varieties,to improve rice quality（Yan et al.2007）.Recent advancements in molecular biology have made it possible to identify genes relevant to starch formation,including the granule-bound starch synthase gene（Wx）,starch branch enzyme genes（Sbe1,Sbe3）,soluble starch synthase gene（Sss1）,isoamylase gene（Isa）,and the rice limit dextrinase or R synthase gene（Pull）,amongst others（Wu 2006; Calingacion et al.2014）.

Recent research has primarily focused on the inheritance of resistance and tolerance,as well as agronomic and phenotypic characteristics of

local rice varieties in the Taihu basin（Diao et al.1999; Li et al.2006; Dikshit et al.2013; Ren et al.2013）.According to Shen et al.（2007,2008）,significant differences in traits exist among local japonica rice varieties; their research confirmed the high phenotypic diversity of local varieties in the Taihu basin（Shen et al.2007,2008）.In a subsequent study at the molecular level,Jin et al.（2006）utilized microsatellite markers to conduct a polymorphic analysis of DNA in 129 local varieties from the Taihu basin.Their results showed that the germplasm of the local varieties of japonica rice contained a rich genetic diversity and large amounts of rare allelic variation（Jin et al.2006）.Similarly,Yu et al.（2009）utilized 45 pairs of simple sequence repeat（SSR）primers to analyze the genetic diversity of 224 local japonica rice varieties in the Taihu basin and revealed 162 allelic variations.Their research concluded that SSR diversity in local japonica rice

varieties

was

relatively

lower

than

that

previously

reported,though,conversely,more rare allelic variations existed（Yu et al.2009）.

In a number of studies into the diversity of rice resources,a variety of techniques,including

amplified

fragment

length

polymorphism

（Sorkheh et al.2016）,restriction fragment length polymorphism（Sun et al.2000）,random amplified polymorphic DNA（Ali et al.2014）,SSR（Lin et al.2012; Melaku et al.2013; Roy et al.2014; Umadevi et al.2014;