【目的】探索靶向捕获测序技术的猪单倍型基因组选择研究效果,为我国猪分子育种提供借鉴。【方法】收集了1267头大白猪的生长性能测定记录和800头大白猪的繁殖记录,利用基于靶向捕获测序技术(genotyping by target sequencing,GBTS)开...【目的】探索靶向捕获测序技术的猪单倍型基因组选择研究效果,为我国猪分子育种提供借鉴。【方法】收集了1267头大白猪的生长性能测定记录和800头大白猪的繁殖记录,利用基于靶向捕获测序技术(genotyping by target sequencing,GBTS)开发的猪50K液相芯片(液相50K)以及靶向捕获重测序数据进行基因型分型,对靶向捕获重测序数据进行单倍型分析,比较固定SNP数目、固定物理间距和靶向block三种单倍型区块划分方法以及单个SNP数据的基因组选择准确性。其中靶向block方法是基于靶向捕获测序技术设计的一种单倍型区块划分方法,通过将靶位点与其上下游400 bp内SNP(mSNP)组合为一个block的方式构建单倍型。本研究对每个单倍型区块采用Beagle5.1进行单倍型推断后,将不同单倍型重新编码为单倍型等位基因,然后利用单倍型剂量模型构建单倍型基因型矩阵,采用一步法模型(ssGBLUP),估计达百公斤体重日龄(AGE)、百公斤活体背膘厚(BF)和总产仔数(TNB)三个性状的基因组育种值。对两个生长性状(AGE和BF)使用双性状动物模型进行估计,对总产仔数性状使用单性状重复力模型。使用年轻群体验证和5倍交叉验证两种验证方法,计算基因组估计育种值与育种值之间的相关系数和基因组估计育种值对估计育种值的回归系数,分别评价单倍型基因组预测准确性和无偏性。【结果】年轻群体作为验证群体的基因组预测结果表明,相较于液相50K SNP,基因型质量控制后,靶向捕获重测序标记数由液相50K的42302增加到了88105,但其对三个性状的基因组选择准确性反而有所下降。通过靶向block方法划分的单倍型区块平均包含SNP 2.08个、单倍型等位基因5.67个。基于三种单倍型区块划分方法进行的单倍型基因组选择准确性都得到了提高,其中靶向block提升幅度最大,AGE、BF和TNB三个性状准确性比液相50K分别提展开更多
With the shrink of the technology into nanometer scale, network-on-chip （NOC） has become a reasonable solution for connecting plenty of IP blocks on a single chip. But it suffers from both crosstalk effects and sing...With the shrink of the technology into nanometer scale, network-on-chip （NOC） has become a reasonable solution for connecting plenty of IP blocks on a single chip. But it suffers from both crosstalk effects and single event upset （SEU）, especially crosstalk-induced delay, which may constrain the overall performance of NOC. In this paper, we introduce a reliable NOC design using a code with the capability of both crosstalk avoidance and single error correction. Such a code, named selected crosstalk avoidance code （SCAC） in our previous work, joins crosstalk avoidance code （CAC） and error correction code （ECC） together through codeword selection from an original CAC codeword set. It can handle possible error caused by either crosstalk effects or SEU. When designing a reliable NOC, data are encoded to SCAC codewords and can be transmitted rapidly and reliably across NOC. Experimental results show that the NOC design with SCAC achieves higher performance and is reliable to tolerate single errors. Compared with previous crosstalk avoidance methods, SCAC reduces wire overhead, power dissipation and the total delay. When SCAC is used in NOC, it can save 20% area overhead and reduce 49% power dissipation.展开更多
基金supported in part by the National Natural Science Foundation of China (NSFC) under Grant Nos. 60606008,60633060, and 60776031the National Basic Research 973 Program of China under Grant No. 2005CB321604+1 种基金the National High Technology Research and Development 863 Program of China under Grant Nos. 2007AA01Z476, 2007AA01Z109 and 2007AA01Z113Co-Building Program of Beijing Municipal Education Commission
文摘With the shrink of the technology into nanometer scale, network-on-chip （NOC） has become a reasonable solution for connecting plenty of IP blocks on a single chip. But it suffers from both crosstalk effects and single event upset （SEU）, especially crosstalk-induced delay, which may constrain the overall performance of NOC. In this paper, we introduce a reliable NOC design using a code with the capability of both crosstalk avoidance and single error correction. Such a code, named selected crosstalk avoidance code （SCAC） in our previous work, joins crosstalk avoidance code （CAC） and error correction code （ECC） together through codeword selection from an original CAC codeword set. It can handle possible error caused by either crosstalk effects or SEU. When designing a reliable NOC, data are encoded to SCAC codewords and can be transmitted rapidly and reliably across NOC. Experimental results show that the NOC design with SCAC achieves higher performance and is reliable to tolerate single errors. Compared with previous crosstalk avoidance methods, SCAC reduces wire overhead, power dissipation and the total delay. When SCAC is used in NOC, it can save 20% area overhead and reduce 49% power dissipation.
