Association analysis of fiber quality traits and exploration of elite alleles in Upland cotton cultivars/accessions(Gossypium hirsutum L.)

Exploring the elite al eles and germplasm acces-sions related to fiber quality traits wil accelerate the breeding of cotton for fiber quality improvement. In this study, 99 Gossypium hirsutum L. accessions with diverse origins were used to perform association analysis of fiber quality traits using 97 polymorphic microsatel ite marker primer pairs. A total of 107 significant marker-trait associations were detected for three fiber quality traits under three different environments, with 70 detected in two or three environments and 37 detected in only one environment. Among the 70 significant marker-trait associations, 52.86% were reported previously, implying that these are stable loci for target traits. Furthermore, we detected a large number of elite al eles associated simulta-neously with two or three traits. These elite al eles were mainly from accessions col ected in China, introduced to China from the United States, or rare al eles with a frequency of less than＆amp;nbsp;5%. No one cultivar contained more than half of the elite al eles, but 10 accessions were col ected from China and the two introduced from the United States did contain more than half of these al eles. Therefore, there is great potential for mining elite al eles from germplasm accessions for use in fiber quality improvement in modern cotton breeding.

Rice Interploidy Crosses Disrupt Epigenetic Regulation, Gene Expression, and Seed Development

Seed development in angiosperms requires a 2：1 maternal-to-paternal genome ratio （2m：lp） in the endo- sperm. When the ratio is disrupted, the seed development is impaired. Rice interploidy crosses result in endosperm failures, but the underlying molecular mechanisms remain unclear. Here, we report that the defective endosperm in rice interploidy crosses was associated with nonadditive expression of small RNAs and protein-coding genes. Interestingly, 24-nt small interfering RNAs were enriched in the 5＇ and 3＇ flanking sequences of nonadditively expressed genes in the interploidy crosses and were negatively associated with the expression of imprinted genes. Furthermore, some PRC2 family genes and DNA methylaUon-related genes including OsMETlb and OsCMT3a were upregulated in the 2x4 cross （polli- nating a diploid ＂mother＂ with a tetraploid ＂father＂） but repressed in the reciprocal cross. These different epigenetic effects could lead to precocious or delayed cellularization during endosperm development. Notably, many endosperm-preferred genes, including starch metabolic and storage protein genes during grain filling, were found to be associated with DNA methylation or H3K27me3, which are repressed in both 2×4 and 4 ×2 crosses. WUSCHEL homeobox2 （WOX2）-Iike （WOX2L）, an endosperm-preferred gene, was expressed specifically in the rice endosperm, in contrast to WOX2 expression in the Arabidopsis embryo. Disruption of WOX2L in transgenic rice by CRISPR/Cas9-mediated gene editing blocked starch and protein accumulation, resulting in seed abortion. In addition to gene repression, disrupting epigenetic process in the interploidy crosses also induced expression of stress-responsive genes. Thus, maintaining the 2m：lp genome ratio in the endosperm is essential for normal grain development in rice and other cereal crops.