SNP frequency, haplotype structure and linkage disequilibrium in elite maize inbred lines.
SNP frequency, haplotype structure and linkage disequilibrium in elite maize inbred lines.
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DOI：
10.1186/1471-2156-3-19
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发表时间：
2002-10-07
期刊：
影响因子：
2.9
通讯作者：
Rafalski AJ
中科院分区：
文献类型：
--
作者：
Ching A;Caldwell KS;Jung M;Dolan M;Smith OS;Tingey S;Morgante M;Rafalski AJ
对玉米祖先种群的近期研究表明，连锁不平衡往往会迅速消散，有时在100个碱基对范围内就会消散。我们着手研究玉米优良自交系中的连锁不平衡和多样性，这些自交系经历了种群瓶颈以及育种者的强烈选择。预计这类种群事件会增加连锁不平衡的程度，但会降低多样性。本研究的结果将为遗传关联研究的设计提供参考。
我们检测了36个玉米自交系中18个玉米基因的DNA多态性的频率和分布，这些自交系被选来代表美国优良玉米育种群体中的大部分遗传多样性。核苷酸变化的频率很高，在非编码区平均每31个碱基对就有一个多态性，在编码区平均每124个碱基对有一个多态性。插入和缺失在非编码区很常见（每85个碱基对有1个），但在编码区很少见。在所有检测的基因座上都能区分出少量（2 - 8个）独特且高度多样的单倍型。在基因内部，构成单倍型的单核苷酸多态性（SNP）位点彼此之间存在连锁不平衡。
在优良玉米种质中，没有发现在几百个碱基对范围内连锁不平衡的下降。这一发现以及相对于中性预期较少的单倍型数量，与育种导致的瓶颈和选择对优良种质库的影响是一致的。单倍型之间的遗传距离较大，这表明玉米祖先具有古老的基因库以及可能存在种间杂交事件。
Recent studies of ancestral maize populations indicate that linkage disequilibrium tends to dissipate rapidly, sometimes within 100 bp. We set out to examine the linkage disequilibrium and diversity in maize elite inbred lines, which have been subject to population bottlenecks and intense selection by breeders. Such population events are expected to increase the amount of linkage disequilibrium, but reduce diversity. The results of this study will inform the design of genetic association studies. We examined the frequency and distribution of DNA polymorphisms at 18 maize genes in 36 maize inbreds, chosen to represent most of the genetic diversity in U.S. elite maize breeding pool. The frequency of nucleotide changes is high, on average one polymorphism per 31 bp in non-coding regions and 1 polymorphism per 124 bp in coding regions. Insertions and deletions are frequent in non-coding regions (1 per 85 bp), but rare in coding regions. A small number (2–8) of distinct and highly diverse haplotypes can be distinguished at all loci examined. Within genes, SNP loci comprising the haplotypes are in linkage disequilibrium with each other. No decline of linkage disequilibrium within a few hundred base pairs was found in the elite maize germplasm. This finding, as well as the small number of haplotypes, relative to neutral expectation, is consistent with the effects of breeding-induced bottlenecks and selection on the elite germplasm pool. The genetic distance between haplotypes is large, indicative of an ancient gene pool and of possible interspecific hybridization events in maize ancestry.
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DOI：
10.1073/pnas.132259199
发表时间：
2002-07-09
影响因子：
11.1
作者：
Fu, HH;Dooner, HK
通讯作者：
Dooner, HK
影响因子：
30.8
作者：
Lindblad-Toh, K;Winchester, E;Lander, ES
通讯作者：
Lander, ES
DOI：
10.1073/pnas.94.13.6809
发表时间：
1997-06-24
影响因子：
11.1
作者：
Gaut, BS;Doebley, JF
通讯作者：
Doebley, JF
DOI：
10.1073/pnas.95.18.10774
发表时间：
1998-09-01
影响因子：
11.1
作者：
Kruglyak, S;Durrett, RT;Aquadro, CF
通讯作者：
Aquadro, CF
影响因子：
10.7
作者：
ArisBrosou, S;Excoffier, L
通讯作者：
Excoffier, L