1) Phenotypic selection (PS)
– based on phenotypic value
2) Marker-based selection (MBS)
– from markers that represent QTL or are linked to QTL
3) Marker-assisted selection (MAS)
(3) selection without laborious fieldwork or intensive laboratory work; (4) selection at an earlier breeding stage; (5) selection for multiple genes and/or multiple traits; (6) whole genome selection.
Paradox of MAS




Qualitative traits and quantitative traits with high heritability are more amenable to MAS than quantitative traits with low heritability, which is generally the case for phenotypic selection as well. Epistasis (or effect of genetic background) and genotype by environment interactions (GXE) can confound progress from MAS just as they do in conventional selection schemes. Efforts to improve the precision of QTL estimation through increased replication and multilocational testing will also increase the efficiency of phenotypic selection, thereby reducing the gains that may be attained through MAS. Catch 22:
种实践中希望在早期选择； ○ 除目标性状外，还需对遗传背景进行选择； ○ 质量-数量性状的选择。
1、标记辅助选择的基本方法 1）前景选择（foreground selection） ——对目标基因的选择 ●单标记
可靠性：取决于标记与目标基因间连锁的紧密程度。如， 标记座位M/m与目标基因座位Q/q连锁，重组率为r，则在F2
marker and QTL 4) The frequency of the QTL (MAS will be more beneficial when the QTL is in low frequency)
Requirements for wide-scale application of MAS
– If phenotypes are poor indicators of genotypes, you cannot map
QTL for use in MAS – If phenotypic data are good, you don‟t need MAS
3. The utility of a marker depends on
– from a combination of phenotypic value and marker information
4) Marker-assisted backcrossing (MABC) 5) Marker-assisted recurrent selection (MARS) 6) Genomic Selection or Genome-wide Selection (GS or GWS)
根据标记基因型M/M获得目标基因型Q/Q的概率为
p=（1-r）2。 选择正确率随重组率增加而迅速降低。
★ 如要求正确率在90%以上，则标记与目标基因间的重
组率必须＜5%。
Genotypes of F2 plants for Xa-21 gene as determined by a PCR marker and progeny tests
和基因的累加等方面。
Tester M & Langridge Breeding technologies to increase crop production in a changing world. Science,2010,V 327:818-822
抗性供体m R源自受体×M S
目的基因与标记连锁（交换值为r） 亲本中的标记带型
with a long generation time – Reduce number of generations in a backcrossing program by selecting for recovery of the recurrent parent genome as well as genes of interest from the donor parent

Validation of QTL in breeding materials
– Multiple markers in vicinity of QTL desirable
Simple, quick, inexpensive protocols for tissue sampling, DNA extraction, genotyping, and data collection Efficient data tracking, management, and integration with phenotypic data Decision support tools for breeders

Genes for multiple traits of interest may also be combined in one cultivar with relative efficiency Marker technologies provide the potential to understand the underlying causes of epistasis and GXE, which could greatly improve selection efficiency
– May permit selection of individual plants

May speed up the breeding process
– May be effective for early generation testing – Selections at the seedling stage can be a great advantage in crops
– optimal design of selection strategies – accurate selection of genotypes
第二节 质量性状的标记辅助选择
大多数情况下，质量性状无需借助于分子标记，但采
用分子标记辅助选择可提高选择效率：
○ 表现型测定难度大或费用太高；
○ 表现型只能在个体发育后期才能测量，而育
2、Most suitable for MAS

Useful if conventional screening methods are laborious, costly, or environmentally dependent
– Selections for disease and insect resistance can be made in the
absence of the pathogen or pest – Greatest potential advantage over phenotypic selection for traits with low penetrance or low heritability

May reduce population sizes needed for phenotypic selection

Pyramid genes for a single trait that could not otherwise be distinguished at the phenotypic level
– Accumulating multiple quantitative trait loci (QTL) for
第十七章 分子标记辅助选择
第一节 分子标记辅助选择的基本原理
第二节 质量性状的标记辅助选择
第三节 数量性状的标记辅助选择
第四节 分子标记辅助选择的挑战与发展策略
传统的育种主要是根据植株的表现型进行选
择，而环境条件、基因间互作、基因型与环境互作
等多种因素都会影响表型选择效率。
育种者在长期的实践中不断探索运用遗传标记
– Select for breeding values summed across many markers without
estimation of QTL
(1) selection without test crossing or a progeny test;
(2) selection independent of environments;
共显 DNA 记的 助选 原理
性 标 辅 择
m R
M S
F1中的标记带型 × F2群体中3种标记带型
RR
RS 2r(1-r) 0.095