籼型血缘渗入对北方粳稻产量和品质的影响

The Effect of indica/Xian Pedigree Introgression in japonica/Geng Rice Breeding in China

【目的】分析籼型血缘渗入对粳稻品种产量和品质的影响,为优化籼型血缘利用的北方粳稻育种方案提供理论基础和基因组资源。【方法】以籼粳交重组自交系(RIL)及从黑龙江省、辽宁省、山东省和江苏省收集的74份不同年代粳稻主栽品种为试材,结合基于Illumina HiSeq2500平台的全基因组高通量测序和多地表型调查,分析籼型血缘对北方粳稻产量和品质的影响,并使用CRISPR/Cas9基因编辑技术对籼型血缘渗入所引入的不利基因进行基因敲除。【结果】分析RIL发现籼型血缘与穗长、粒长呈显著正相关,与碾磨品质呈负相关,其中,与整精米率达到显著水平。籼型血缘在江苏省与直链淀粉含量呈显著负相关,与粗蛋白含量呈显著正相关。籼型频率与粒形的相关性随着纬度的增加而增强,而与穗长和整精米率的相关性随着纬度的增加而减弱。通过调查粳稻主要稻区不同年代主栽品种,发现籼型血缘渗入位置和比例并不是均匀分布在12条染色体上,在第1、10、11和12染色体上,籼型血缘分布较多。江苏省和辽宁省主栽品种的籼型血缘显著高于黑龙江省和山东省,而且2000年后育成的品种籼型血缘显著高于2000年之前的品种。各粳稻区不同年代主栽品种籼型血缘渗入显著增加了每穗粒数,籼型血缘渗入区域中包含多个抗性和育性相关基因。在盐丰47的第5染色体上有一段籼型血缘渗入片段,包含籼型粒型调控基因GS5和籼型垩白调控基因Chalk5,增加了盐丰47的千粒重,但影响了其垩白性状。应用CRISPR/Cas9技术敲除盐丰47的Chalk5,纯合基因编辑植株的粒形与盐丰47相似,其垩白性状得到了显著改善。【结论】籼型血缘渗入主要通过增加每穗粒数增加粳稻产量潜力,但对碾磨品质有负面影响。通过全基因组高通量测序挖掘品种不良等位基因,结合CRISPR/Cas9基因编辑打破籼粳杂交育种中的遗传累赘是一种高效的育种辅助手段,可以针对目标性状进行快速准确的改良。

【Objective】To demonstrate the impact of indica/Xian(XI)pedigree introgression on the yield and quality of japonica/Geng(GJ)rice varieties,providing a theoretical basis and genomic resources for optimizing XI pedigree introgression breeding programs in northern GJ rice.【Method】In this study,the whole genome sequence on Illumina platform was employed to elucidate the effects of XI pedigree introgression on the yield and quality of rice in Northeast China were analyzed using recombinant inbred lines(RIL)derived from the cross between XI and GJ varieties,and 74 major GJ varieties grown from Heilongjiang,Liaoning,Shandong,and Jiangsu provinces as test materials.Using CRISPR/Cas9 gene editing technology to knock out the unfavorable genes introduced by XI pedigree introgression.【Result】Analysis of RIL revealed a significant positive correlation between XI pedigree introgression and panicle length,grain length,and a negative correlation with head rice ratio.XI pedigree introgression was significantly negatively correlated with Amylose content,and significantly positively correlated with protein content in Jiangsu.With the increase of latitude,the correlation efficiency between XI pedigree introgression and grain shape increased,while the correlation between XI pedigree introgression and panicle length and head rice ratio decreased.The genomic fragments of XI pedigree introgression are unevenly distributed across different chromosomes and are more abundantly present on chromosomes 1,10,11,and 12.The XI pedigree introgression of the major cultivars in Jiangsu and Liaoning provinces is significantly higher than that in Heilongjiang and Shandong provinces,and the XI pedigree introgression of the cultivars after 2000 is significantly higher than that before 2000.The XI pedigree introgression includes multiple resistance and fertility-related genes.The project identified an XI pedigree introgression fragment on chromosome 5 of YF47,including the XI type grain regulatory gene GS5 and XI type chalkiness regulatory gene Chalk5,which increased the 1000 grain weight of YF47 but affected its chalkiness-related traits.The project uses CRISPR/Cas9 technology to knock out the Chalk5 gene of YF47.The grain shape of the homozygous gene editing plants is similar to those of YF47,and its chalkiness character has been significantly improved.【Conclusion】The XI pedigree introgression mainly increases the yield potential of GJ rice by increasing the number of grains per panicle,but has a negative impact on milling quality.Exploring the unfavorable alleles in varieties through high-throughput genome sequencing,combined with CRISPR/Cas9 gene editing,to break the genetic drag in breeding using the cross between XI and GJ,is an efficient breeding strategy that can quickly and accurately improve target traits.