AUTHOR=Kong Weilong , Deng Xiaoxiao , Liao Zhenyang , Wang Yibin , Zhou Mingao , Wang Zhaohai , Li Yangsheng 

TITLE=De novo assembly of two chromosome-level rice genomes and bin-based QTL mapping reveal genetic diversity of grain weight trait in rice

JOURNAL=Frontiers in Plant Science

VOLUME=13

YEAR=2022

URL=https://www.frontiersin.org/journals/plant-science/articles/10.3389/fpls.2022.995634

DOI=10.3389/fpls.2022.995634

ISSN=1664-462X

ABSTRACT=<p>Following the “green revolution,” <italic>indica</italic> and <italic>japonica</italic> hybrid breeding has been recognized as a new breakthrough in further improving rice yields. However, heterosis-related grain weight QTLs and the basis of yield advantage among subspecies has not been well elucidated. We herein <italic>de novo</italic> assembled the chromosome level genomes of an <italic>indica/xian</italic> rice (Luohui 9) and a <italic>japonica/geng</italic> rice (RPY geng) and found that gene number differences and structural variations between these two genomes contribute to the differences in agronomic traits and also provide two different favorable allele pools to produce better derived recombinant inbred lines (RILs). In addition, we generated a high-generation (&gt; F<sub>15</sub>) population of 272 RILs from the cross between Luohui 9 and RPY geng and two testcross hybrid populations derived from the crosses of RILs and two cytoplasmic male sterile lines (YTA, <italic>indica</italic> and Z7A, <italic>japonica</italic>). Based on three derived populations, we totally identified eight 1,000-grain weight (KGW) QTLs and eight KGW heterosis loci. Of QTLs, <italic>qKGW-6.1</italic> and <italic>qKGW-8.1</italic> were accepted as novel KGW QTLs that have not been reported previously. Interestingly, allele genotyping results revealed that heading date related gene (<italic>Ghd8</italic>) in <italic>qKGW-8.1</italic> and <italic>qLH-KGW-8.1</italic>, can affect grain weight in RILs and rice core accessions and may also play an important role in grain weight heterosis. Our results provided two high-quality genomes and novel gene editing targets for grain weight for future rice yield improvement project.</p>