Genome-wide identification of the pectate lyase(PEL)gene family members in Malvaceae,and their contribution to cotton fiber quality

Pectin is a major constituent of the plant cell wall.Pectate lyase(PEL,EC 4.2.2.2)uses anti-β-elimination chemistry to cleave theα-1,4 glycosidic linkage in the homogalacturonan region of pectin.However,limited information is available on the comprehensive and evolutionary analysis of PELs in the Malvaceae.In this study,we identified 597PEL genes from 10 Malvaceae species.Phylogenetic and motif analyses revealed that these PELs are classified into six subfamilies:Clades I,II,III,IV,Va,and Vb.The two largest subfamilies,Clades I and II,contained 237 and222 PEL members,respectively.The members of Clades Va and Vb only contained four or five motifs,far fewer than the other subfamilies.Gene duplication analysis showed that segmental duplication played a crucial role in the expansion of the PEL gene family in Gossypium species.The PELs from Clades I,IV,Va,and Vb were expressed during the fiber elongation stage,but nearly all PEL genes from Clades II and III showed no expression in any of the investigated fiber developmental stages.We further performed single-gene haplotype association analysis in 2,001G.hirsutum accessions and 229 G.barbadense accessions.Interestingly,14 PELs were significantly associated with fiber length and strength traits in G.barbadense with superior fiber quality,while only eight GhPEL genes were found to be significantly associated with fiber quality traits in G.hirsutum.Our findings provide important information for further evolutionary and functional research on the PEL gene family members and their potential use for fiber quality improvement in cotton.

Genomic insights into the genetic basis of cotton breeding in China

The excellent Upland cotton(Gossypium hirsutum)cultivars developed since 1949 have made a huge contribution to cotton production in China,the world's largest producer and consumer of cotton.However,the genetic and genomic basis for the improvements of these cotton cultivars remains largely unclear.In this study,we selected 16 Upland cotton cultivars with important historical status in Chinese cotton breeding and constructed a multiparent,advanced generation,intercross(MAGiC)population comprising 920 recombinant inbred lines.A genome-wide association study using the MAGIC population identified 54 genomic loci associated with lint yield and fiber quality.Of them,25(46.30%)pleiotropic genomic loci cause simultaneous changes of lint yield and/or fiber quality traits,revealing complex trade-offs and linkage drags in Upland cotton agronomic traits.Deep sequencing data of 11 introduced ancestor cultivars and publicly available resequencing datasets of 839 cultivars developed in China during the past 70 years were integrated to explore the historical distribution and origin of the elite or selected alleles.Interestingly,85%oftheseelitealleles were selectedandfixed fromdifferent Americanancestors,consistentwithcotton breeding practices in China.However,seven elite alleles of native origin that are responsible for Fusarium wilt resistance,early maturing,good-quality fiber,and other characteristics were not found in American an-cestors but have greatly contributed to Chinese cotton breeding and wide cultivation.Taken together,these results provide a genetic basis for further improving cotton cultivars and reveal that the genetic composition of Chinese cotton cultivars is narrow and mainly derived from early introduced American varieties.

A new model system for cotton indoor genetic and genomic research

Dear Editor,As an important fiber and oil crop,cotton has gradually developed into a model plant for studying fiber or seed trichome and polyploid evolution.Thus,strengthening cotton research is essential.Significant progress has been made in the research of cotton genomics(Hu et al.,2019;Huang and Zhu,2021;Wen et al.,2022).However,further research has been hindered due to its long growth period(usually 4–6 months per generation)and large plant size(usually 0.8–1.5 m in height).