Genomic selection for fruit quality traits in apple (Malus×domestica Borkh.).
Genomic selection for fruit quality traits in apple (Malus×domestica Borkh.).
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DOI：
10.1371/journal.pone.0036674
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发表时间：
2012
期刊：
影响因子：
3.7
通讯作者：
Carlisle C
中科院分区：
文献类型：
--
作者：
Kumar S;Chagné D;Bink MC;Volz RK;Whitworth C;Carlisle C
苹果（Malus× arctica Borkh.）一年多前发表，帮助开发了一种8 K SNP芯片，以协助实施基因组选择（GS）。在苹果育种计划中，GS可用于获得基因组育种值（GEBV），用于选择下一代亲本或在非常早期阶段选择进一步测试为潜在的商业品种。因此，GS有可能通过缩短世代间隔或增加选择强度而显著提高育种效率。我们评估了GS的准确性，在人口中产生的1120苗从析因交配设计的四个女性和两个男性的父母。使用包含8，000个单核苷酸多态性（SNP）的Illumina Infinium芯片对所有幼苗进行基因分型，并对各种果实品质性状进行表型。使用随机回归最佳线性无偏预测（RR-BLUP）和贝叶斯LASSO方法获得GEBV，并使用交叉验证方法比较其预测未观察到的BLUP-BV的准确性。两种方法的准确度非常相似，不同的水果品质性状从0.70到0.90不等。与传统的BLUP选择相比，GS的单位时间选择反应非常高（>100%），特别是对低遗传力性状。全基因组范围内相邻SNPs之间的平均估计连锁不平衡（LD）为0.32，LD在长范围内衰减相对缓慢（在100 kb和1,000 kb处r2分别为0.33和0.19），有助于GS的更高准确性。 估计SNP效应的分布揭示了大效应基因可能具有多效性效应。这些结果表明，基因组选择是一个可靠的替代传统选择的果实品质性状。
The genome sequence of apple (Malus×domestica Borkh.) was published more than a year ago, which helped develop an 8K SNP chip to assist in implementing genomic selection (GS). In apple breeding programmes, GS can be used to obtain genomic breeding values (GEBV) for choosing next-generation parents or selections for further testing as potential commercial cultivars at a very early stage. Thus GS has the potential to accelerate breeding efficiency significantly because of decreased generation interval or increased selection intensity. We evaluated the accuracy of GS in a population of 1120 seedlings generated from a factorial mating design of four females and two male parents. All seedlings were genotyped using an Illumina Infinium chip comprising 8,000 single nucleotide polymorphisms (SNPs), and were phenotyped for various fruit quality traits. Random-regression best liner unbiased prediction (RR-BLUP) and the Bayesian LASSO method were used to obtain GEBV, and compared using a cross-validation approach for their accuracy to predict unobserved BLUP-BV. Accuracies were very similar for both methods, varying from 0.70 to 0.90 for various fruit quality traits. The selection response per unit time using GS compared with the traditional BLUP-based selection were very high (>100%) especially for low-heritability traits. Genome-wide average estimated linkage disequilibrium (LD) between adjacent SNPs was 0.32, with a relatively slow decay of LD in the long range (r 2 = 0.33 and 0.19 at 100 kb and 1,000 kb respectively), contributing to the higher accuracy of GS. Distribution of estimated SNP effects revealed involvement of large effect genes with likely pleiotropic effects. These results demonstrated that genomic selection is a credible alternative to conventional selection for fruit quality traits.
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DOI：
10.1186/1297-9686-42-5
发表时间：
2010-02-19
期刊：
Genetics, selection, evolution : GSE
影响因子：
--
作者：
Habier D;Tetens J;Seefried FR;Lichtner P;Thaller G
通讯作者：
Thaller G
DOI：
10.1111/j.1365-313x.2006.02964.x
发表时间：
2007-02
期刊：
The Plant journal : for cell and molecular biology
影响因子：
--
作者：
Espley RV;Hellens RP;Putterill J;Stevenson DE;Kutty-Amma S;Allan AC
通讯作者：
Allan AC
影响因子：
3.7
作者：
Chagné D;Crowhurst RN;Troggio M;Davey MW;Gilmore B;Lawley C;Vanderzande S;Hellens RP;Kumar S;Cestaro A;Velasco R;Main D;Rees JD;Iezzoni A;Mockler T;Wilhelm L;Van de Weg E;Gardiner SE;Bassil N;Peace C
通讯作者：
Peace C
影响因子：
5.4
作者：
HILL W G;ROBERTSON A
通讯作者：
ROBERTSON A
影响因子：
3.3
作者：
Habier, D.;Fernando, R. L.;Dekkers, J. C. M.
通讯作者：
Dekkers, J. C. M.